1. The Hardbody pickup used sealed beams, and you can get conversion housings/LEDs/whatever for sealed beams. You need the grille, side markers, and buckets from a Hardbody to make it work. I remember seeing conversion housings in the Pathfinder sad-eye shape a while back--pre-Covid, probably, now I'm thinking about it--but I haven't seen those around in a while. Also look into relaying the headlights. The factory setup puts a lot of stress on the headlight switch, and probably loses a little voltage to the bulbs while it's at it.
2. Mine's got the slushbox, so no firsthand experience here, but I generally see MT-90 called out.
3. If the EGR is stuck open, and it doesn't have California emissions (California trucks have a sensor that'll notice it's gone and throw a code), then sure, delete it. Otherwise, leave it alone. It's supposed to improve the fuel economy a little. There is no benefit to getting rid of the evap can, unless you want the truck to smell like gas. This isn't a malaise era clunker (or a modern diesel) where the smog gear is holding it back and/or trying to kill it.
4. I think the fan from a Ford Taurus was popular for a while. Should be some old threads about that around here somewhere. Sounds like the clutch fan does better under heavy load, though. You may want to upgrade your alt if you put an e-fan on it, the stock alt's only 70A. I've got a 90A alt for a '93 Maxima (SOHC) on mine, bolted right up. I'm still running the clutch fan on mine.
5. I think I got the platinum NGK plugs for mine. Don't remember the numbers, whatever Rockauto said it took. Don't buy them on Amazon, sounds like they have a problem with people selling counterfeit spark plugs, because of course that's a thing.
6. They do use ATF. The early service manuals say to run the same oil that's in the transmission, but the later ones say to run ATF either way.
7. IIRC the 300ZX exhaust studs are supposed to be tougher. I have a set of those that I bought for mine years ago. Never got excited about putting them in. While you're messing with the exhaust, check for an exhaust leak from the Y pipe, blowing up at the floor. They tend to leak there, rust out the floor, and then set the carpet on fire.
8. These trucks aren't quick at the best of times, but the noise is worth tracking down. Could be a lot of things, tough to say without hearing it. Could be rattling heat shields on the exhaust, could be accessory or idler bearings going out. Your tuneup plans may help with the power. Check the timing while you're in there.
I took an auto hub all to bits once, in hopes that a good clean and some fresh grease would bring it around. Turned out the clutch inside was worn way past spec, and the old grease was the only thing making it work as much as it did. The truck it was on had about half the mileage of yours. If you plan to use the four wheel drive, huck the auto hubs in the bin and get manual hubs! The autos were a neat idea, but there's a reason nobody makes them anymore.
Oh, and download a service manual! The '90 manual from cardiagn.com is the closest to your year that I'm aware of.