I cannot comment on your smog issues. However i have a 3.4L tacoma motor that originally had an automatic behind it.
Swapped this into my 90 4runner with a 5speed.
I have all the automatic connectors not plugged into anything,i need to do something with them, but they are not plugged to the ecu anymore so they arn't hurting anything. I also never hooked up the reverse lights.
However all i did was jump the wires for the park/neutral saftey switch and its been fine for the last 30,xxx miles or so. I think i remember people saying that if you do this, when you put the rig in reverse it will trigger a CEL. Unsure if it is true or not.
http://www.ncttora.com/fsm/Here is a link, you should be able to find the wiring diagrams here.
I cannot verify if you will have a check engine light or smog problems, all i can say is you will be able to get it to run. Mine is not the best example because it is not the factory wiring harness anymore so yours might act different. I just wanted to post to say i have been using an automatic ECU this way since i did my swap
