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If you haven't solved this issue yet, check the fuel line that connects the two fuel rails. It's located right behind/under the distributor at the front of the engine; this leak is common on wd21s. I recently had the same problem so tightened up the clamps; no more leaking and no more smell!
I have the exact same problem - locked in third gear (or second if you manually put it into "1st") until it warms up and is restarted. In my case, it happens when it's below 40ish. There's been a few times where it's been cold (single digits) where it started and drove fine without warming up. I ran the diagnostic process and got codes 1 and 2: speed sensor and revolution sensor, according to the manual. OP, does your speedo jump when you start the car? It's something that I've noticed mine will do when cold. The speedo will also jump when I press the brake pedal or turn the lights on. This could be unrelated but my guess is that it's a wiring issue with the speed sensor.
I'm having a similar issue except that I've only noticed the speedo jumping periodically when I turn my headlights on. Often, the dash lights won't come on at all or until a few minutes have passed. My temp gauge does work, so that's most likely an unrelated issue. I also have a grinding/vibrating noise when taking off and hitting a certain rpm range but I attributed that to the exhaust system vibrating against something. As to starting off in third gear and not shifting into overdrive, that would indicate it's in "failsafe" mode. I did follow the steps in the manual to get the transmission code to no avail: none of them were reading incorrectly. It's difficult to troubleshoot though because if you try it without the car started (after it's been driving correctly), then the codes won't be set. If you start the vehicle so that it's running incorrectly then shut it off to check the codes, it seems to reset them as the next time you start, it runs correctly. I live in cooler weather up here so I usually have to wait until it's warm to restart and fix the issue. I'll try to troubleshoot it again tonight to see if I can come up with any codes. Also, did you ever find anything else about the issue yourself?