eh, thats EXACTLY the symptom i had. check your tranny oil!!! a brief story:
i did my swap, la di da, everything went smoothly for the most part. filled ALL my fluids/oils/etc... i started noticing a slight vibration on my way to class one day, thought nothing of it, on my way home, it got a little worse, but i was a mile from home, so i continued driving (about 65mph). about a half mile from my house, black smoke started to billow into the cabin of the car through the shifter hole. the stick was HOT, and it smelled like burning gear oil.
well, to make a long story short, basically what happened, was the rear seal in my tranny shit the bed, and i didnt even know it because all the tranny oil stuck itself to the undercarriage of the car, rather than dripping down on the ground, so i had no idea i was losing gear oil. when i was stopped, in neutral, clutch out, i would hear almost a jingling noise, and when i pressed the clutch in, NOTHING. silent as it should be.
i have a w58 in my turbo supra, but i'm sure it *COULD* be the same thing. check your gear oil!
-shaeff