Slartibartfast

I don't know crap about the R52, but I did spend entirely too long troubleshooting a trailer wiring fault on my mom's Lexus that resolved itself when I turned the ignition on. I guess it's got a powered trailer light controller? Something to check if you've been testing with the key off.

AFAIK, no. The only time I've heard of exhaust studs and coolant in the same sentence is when someone goes to drill out a broken one and misses.

IMO better to pull the upper cover off and get a proper look, than to drill a hole and potentially drop a bunch of swarf into the belt so you can squint at a screen.

I am a little confused on what you're trying to achieve. Are you looking for something in particular, or just keeping an eye on things? +1 for a grommet if you do start making holes. My dad's Tundra had an open hole in the timing cover (previous hack lost a grommet), and a mouse got in. It turns out skipping two teeth is not enough to kill a 2UZ-FE, but making one skip two teeth is absolutely enough to kill a mouse.

The bearings go bad. I took apart a failed dizzy from an Xterra last year. The upper bearing had ground itself to dust.

My spare IACV looks about like how you described yours. Half open at room temp. I connected 12v across the heater, and ~5 minutes later, it closed up. Left is cold, right is after powering the heater. I didn't try the freezer test, but the cutout does look like it should open a lot more than it is at room temp. Injectors would make sense. I've got one or two marginal ones on mine. One crapped out entirely once, consistent misfire, tested open circuit, then came around the next day and worked like nothing happened. It's been working since, so I haven't gotten around to replacing it. But I have noticed a little stumble from time to time, which I suspect is related. You can check all six injectors from the harness plug on the passenger's side valve cover. Of course that'll only tell you if the coils are good, not whether they're plugged up or spraying weird. But it's a start.

I'd say you found why the last guy sold it! Now that it's self-healed, you may have an uphill battle trying to track down the problem. The first thing to do is check it for codes. No way you lost drive and power to the dash without it setting a code somewhere, and that'll give you a lot more to work with than you have now. Do that before chasing any of my speculations below. (Also keep in mind that I don't know the R51 for crap. This could be a common issue that I haven't heard of.) Without codes, I would start by chasing the overcharging issue. The starting/charging section of the service manual shows that the alternator is controlled by the intelligent power distribution module, which takes orders from the ECM, which watches a current sensor on the battery ground cable. So that's narrowed it down less than you'd hope. Given you're having power distribution issues, and the truck has a power distribution module, I'd be suspicious of the IPDM. This guy reckons the early IPDMs have bad solder joints and do weird stuff when they crap out. Naturally he's selling IPDMs, so, do your own research. If the alt loses its signal from the IPDM, it's supposed to default to its internal regulator, like an old-school non-computer-controlled alt. The regulator in the alt could be bad, but that wouldn't explain the other issues. I would also have a look at ground cable on the battery. That's where the sensor is for the smart alt, and bad grounds can cause all kinds of weirdness besides.

Check your trans fluid level. The fluid level rises slightly as it warms, so if it's very low, the pump might be sucking air for that first 5-10 minutes, until the fluid gets some heat in it. I haven't seen this on a Pathy, but I worked on an S10 pickup with similar symptoms. Drove normally when warm, slipped real bad when cold. The trans fluid was super low, and smelled burned from the slipping. Fixed the leak, fresh fluid, and it was fine again. Hopefully yours bounces back as easily. There's a procedure to set the trans fluid level. Warm it up, park on flat ground, run it through the gears, check it with the engine running, add fluid through the dipstick tube as needed. At least that's how I remember it. Download the AT section of the service manual from Nicoclub, it'll have the instructions. I'm not sure if yours is an R50 or an R51 (IIRC the changeover year was different in your market?), so make sure you're looking at a manual for the correct chassis, not necessarily the correct year. If it's got a solid rear axle, it's an R50. I'd use the '04 manual. If it's IRS, it's an R51, so use the '05. If the fluid level and condition are OK, check it for trouble codes. The computer should have some idea of what's wrong. The AT section of the service manual also has troubleshooting for each code. The manual assumes you have dealership-level scan tools, but there's usually a workaround or a "without Consult" option in there somewhere.

It does make sense that a low idle when the engine is cold would be giving you issues. The high idle is there for a reason. But I assume you didn't smog it cold, and I would expect it to clear up as the engine warms up. It's supposed to come off high idle once it's warmed up anyway. Maybe the computer could be doing something weird if it's letting little or no air through the AAC due to the IACV being stuck open, with the idle still above its target? Maybe someone somewhere down the line meddled with the idle screw to try and mask the bad IACV, and that's making it worse? I still wouldn't expect that to manifest as a misfire under any condition but cold idle. In any case, it does sound like you've found something wrong. Absent any other smoking gun, might as well chase that one, I guess. I have an IACV on a spare plenum. I have no idea if it's good, but if you want I can pop it open and see if it's how you describe yours or not.

EF&EC-14 explains how the idle control components work. The plate in the IACV (the tall one that sticks up) opens when the engine is cold to raise the idle speed. There's a heater inside (that's why it's got the electrical connector) which closes it over time. If it was bad, you would either have a high idle all the time (stuck open), or no high idle when cold (stuck shut). I don't know how much it should open and close from external heating/cooling (surely the heater inside is more effective), but, yeah, if yours is mostly closed at room temp with no power going to it, that ain't right. I'd expect it to be wide open when cold unless it's gunked up or the bimetal that moves the shutter is broken. The IACV-AAC (the one built into the block with the idle adjust screw) is the one that's pulsed by the computer to do the fine-tuning. I'm not sure why there are two valves for the same function. Maybe it was easier to add another valve than it was to add another function to the computer.

No worries! Sometimes the service manual buries stuff in weird places. Good luck with it, hopefully it's not the sending unit.

There's a window lockout switch on the driver's switch panel. Make sure that's not engaged. I'm not seeing a relay in the power window circuit (BF section of the service manual), but there is a circuit breaker that could give you issues. Looks like it's behind the driver's kick panel. Not super far from the flasher, but probably not what you unplugged by mistake.

Look for vacuum leaks, and check the tube from the throttle body to the airbox.

Download the '94 service manual off Nicoclub and take a look in the EL section. EL-40 has shows how to check the cluster. EL-41 shows how to check the sending unit. Should get you started at least!

I'd be surprised if the idle controls made it misfire like that. A vacuum leak, maybe, but the idle air control pulls through the same maf as the rest of the air going into the engine. If it was stuck, you'd get a high or a low idle, but it shouldn't be screwing up the mixture, unless it was borked bad enough to suck air air from the engine bay. Have you checked the rest of the plugs? Might tell you which cylinder is acting up.

I ran mode 2 on mine today. Same as yours, both lights flash. So the computer thinks the mixture is okay, for whatever that's worth. And yeah, OBD1 is a pain.

EF&EC 26 of the '95 FSM says that in mode 2, at 2k rpm, no load, warm engine, the red and green lights should flash, together, more than five times in ten seconds. I don't know why they didn't list that spec in the description for the test modes. I don't know what to make of your twenty seconds on/four seconds off. Trying and failing to enter closed loop? Are you checking at idle or at the 2k rpm spec'd? They don't stay in closed loop at idle, or at least mine doesn't. But I wouldn't expect that result at idle, either. I've got some driving to do tomorrow anyway. I'll set it to mode 2 after and see what derblinkenlightzen have to say. I'm reminded of the usual failure symptoms of the distributors in these. Runs fine when it's cold, starts running like crap as it warms up. Ignition misfires could explain both the high hydrocarbon readings and the rough running. But from what I've read, those tend more towards stalling out and not running at all. Could be that the cold high idle is just masking whatever is wrong with yours, and that's why it gets worse as it warms up.

The '03 service manual says the cam sensor code (P0340, P0345) is set if the computer doesn't see a cylinder number signal in the first few seconds of cranking (could be due to a low battery or weak starter not turning it over fast enough), or during engine running, or if the pattern of that signal is "not in the normal pattern." It suggests checking the sensors, connectors, battery, starter, and the intake camshaft. The manual has some troubleshooting instructions that might be worth going through to rule out the wiring. (The manual is a free download from Nicoclub, and you want the EC section, page 357.) Could be a harness got pinched or a connector broke during the head gasket job. Outside of the manual--assuming all that stuff tests normal--I suspect your timing chain is off by one tooth on the bank that's coding. I suspect this because my dad's Tundra threw a cam sensor code when its timing belt slipped. The sensor was fine, but I guess the timing being a tooth off put the sensor's signal outside of what the computer considered normal, and it wasn't programmed to check for cam/crank correlation, so it blamed the sensor. I don't see a correlation code in the '03 R50 manual, either. And we know someone's been into your timing recently, because a head was off, which was when the issue began. (That's a long way of saying +1 to Adam's thought that the mechanic put it back together wrong.) It's weird that it's taking an hour for the code to appear. I've heard of codes only tripping after a fault is detected however many times. Maybe it just takes an hour for the computer to admit that it has a problem? I would check for pending codes (assuming your scanner can do that--my cheap one can) and see if the code pops as pending soon after startup. And yeah, the VG is a gutless wonder, but I do not envy the complexity of more modern engines.

Hopefully yours don't look like that! A couple did in the VG33 I was going to put in mine, and some of the missing material had found its way past the pickup screen and chewed up the oil pump. The crank and cam bearings were all shot, I assume from low oil pressure. It still ran surprisingly well.

I had a whistle from the intake tube on mine a while back. Drove me nuts. Near as I could tell, it was the sharp edge on the bung that the pipe feeding the idle air control goes into. I "reshaped" it a little with a big drill bit and it's been quiet since. Engine ran the same whether it was whistling or not, though.

Maybe dripping fuel from an injector, or leakage from the pressure regulator into the intake? I'm still trying to think of what would make it oscillate. Also thinking about it again, I would expect a vac leak to cause NOx issues, not HC.

The transfer case takes ATF (Dex-Merc), and the manual transmission takes GL-4 75W90. Make sure it's GL-4! GL-5 rated oil (which is much more common) will eat the synchros. The drain plugs should be pretty obvious once you're under the truck.

Bouncing back and forth sounds more like an EFI issue than a cat issue to me. Lean condition--check the vacuum lines, the intake tube between the MAF and the throttle body, and the MAF itself. If the MAF is covered in schmutz, it'll read less air than is actually going past it.

I'm running a Magnefine on mine as well. I don't know that it's strictly necessary, but I wanted to give my high-mileage slushbox every chance I could, especially after seeing a little glitter in the fluid when I flushed it. I routed the lines on mine so the fluid goes from the trans, through the stock cooler in the rad, through the aux cooler, through the filter, then back to the trans. My thinking was that the OE cooler can only bring the fluid temp down to the coolant temp, so it should be the first stage. I put the filter on the return side just in case the cooler (which was not new when I installed it) had some schmutz in it. That I don't know. But I've had the filter on mine for the last 30k miles, and it hasn't complained.

So it's going back and forth between good and high? The mixture's actually supposed to bounce back and forth a little when it's in closed loop, that's how it controls the mixture with a narrowband oxygen sensor. Maybe the sensor's on its way out and it's responding very slowly? There is a test mode for the oxygen sensor, might be worth running that to see if the light's flashing like it should. Some codes don't trip the light, so I'd run those too on the off chance.