I have a 1990 tracker that I just did a JDM engine replacement in. I got for $600 because the motor had a blown head gasket, and the owners didnt know how to replace a head gasket. It ran when I got it, and the previous owners had taken very good care of it, and they kept it in the garage so it has no sun or weather damage. Any ways, it sits in my garage taken apart for about 3 months while I try to get enough money to fix the engine when my dad offers to help me get a JDM engine for it. We get the jdm engine and I install it. I get it to start and register it. Today is my 4th day driving it. It does this wierd thing where when it is warming up, it surges up and down anywhere from 500 to 1000 rpm, all the while the vacuum diaphragm that makes the throttle open for cold idle is not touching or moving the throttle, so it must be purely the fuel mixture. And when it does this, a sort of unburnt gas smell comes from the exhaust. When I take the vacuum line off of the map sensor, it stops surging but runs roughly. It also surges when the engine cools down after going down a hill or when the engine isnt creating as much heat because it isnt under load, or when I have the heater on, which brings down the engine temp. Is this a common problem for these TBI 1.6 engines. Any help would be much appreciated.

very common problem

The throttle opener should hold the throttle open a bit when the engine is turned off. The vacuum from the engine (under control from the ECU) pulld it away from the stop when its warm, yours may be stuck. Check all the vacuum pipes and all the earths also.

Is it common for the computer to go out on these. On mine, it looks like the ecu under the dash has been replaced. The wierd thing about the rpms surging on mine is that the throttle is not moving and the diaphragm that holds the throttle open when the engine is off is not holding the throttle open or contacting the screw on the throttle when it is surging. From looking at the manual, the only things I can think it could be are the air bypass valve or the EGR. Either way, I need to get it to pass smog, and I hope what it is doing wont affect its passing the smog check. 

my 89 does that surgeing, and it did better on the smog test than my 99 tacoma with a V6, so you should be ok.

 Have you checked the exhst man for cracks or tried a good 02 sensor. I had a 92 16 valve that started doing the same thing after jumping it. The exhst man cracked and threw off the 02 sensor. My 91 8 valve had a bad gasket at the header and did the same type thing but not as bad. On both of them I fixed the leaks and it went away. Don't know if I just got lucky or if this was the problem.  By the way, I chased lots of items before finaly fixing the exhst not beleving that could be the prob.
    Good luck  Joe