[LunchboxCritter]

I have a suggestion that is far from the normal "it's got to be a vaccum leak". I had a similar issue with my car after doing my swap. I tried testing and adjusting BAC, TPS, MAF, hunted leaks, swapped ecu's, etc. My car would bounce at idle once it was up to operating temp. It would bounce between 500 or 600 rpm to 1200 or 1500 rpm. I adjusted stuff until I had it down to bouncing only a few hundred rpms. The car would idle pretty steady around 1200 rpm with the clutch pushed down, but it would shake like I had a fouled spark plug. It was driving me crazy.

I finally figured out that I had wired the neutral switch to the wrong wires on my harness (jspec TII had different connections then my NA harness). Once I fixed that the car works great. I simply had to adjust the idle screw and tps a few times to get it idling at a steay 800 rpm. I'm guessing that if your neutral switch was to malfunction it would cause similar symptoms as I have described. Testing it is fairly simply, it should show continuity in neutral and none in any gear.

I don't know if this helps at all (might just give you something else to rule out), and don't ask why a manual transmission has a neutral switch and a clutch safety switch (still scratching my head over that).