i would try resetting the ECU, too. take the fuse out and disconnect the battery for a time. not sure the exact process, sorry. also, yeah, check the idle speed & fuel pressure. is your butterfly valve well lubed and adjusted? is your intake manifold nasty & dirty? try totally cleaning out the intake manifold & butterfly valve, with the car kinda tilted on a hill so the cleaner goo runs out, instead of in, the intake. then, do a total re-adjustment of your throttle cable. If it's a swap, you may not have the right cable(?).
can you tell if the clutch is totally disengaging? after my swap, the clutch started having problems. I think if I had let it go any longer, I probably would have had the same symptoms. My clutch was not disengaging properly... to the point where I would be all the way to a stop, and the engine would bog, meanwhile not letting me shift out of gear. Once the engine died, however, I could shift into 1st, and starting the car let me notice a jerk on the drivetrain and a ½" drop in the clutch pedal, as the engine turning over was forcing the clutch to disengage. I'll try to think of what else it might be.....
-x