1994 Ford Taurus High and Erratic Idle

After removal/installation of engine/transmission for trans repair I now have an idle problem. At start up the engine races very high (2000rpms?). After a moment it settles down to apprximately 1100 rpms and every couple of minutes it sound like its going to stall out. I've eliminated (i think) vaccum line leaks by plugging ports at the plenum and replaced the IAC valve to no avail. Could I have damaged the intake manifold gaskets or head gaskets when lifting the engine-the lift points are on the heads. I tried to be gentle with the wiring but it is an old car and I live in the desert, I'm afraid the wiring insulation may have cracked off. When I unplug the IAC valve the RPM's seem to come down to what seems right. I also installed a VAPS rack and pinion while I had access but unplugging that doesn't have any effect. Where should I be looking for the source of this problem? Out of frustation and stupidity I put my newly rebuilt trans into gear while the engine raced and now I'm looking at buying a new one.