Ok so here is the deal:
The last autocross I competed in, at the end of my last run when I was driving back to the parking area at a low rpm in 2nd gear I heard a horrible noise, kinda like a grinding. I shut off the car, and let it sit for an hour or so (I had work duty that heat) and when I got in it to go home, the noise was basically gone, but instead 2nd (and 4th) gear started making a whirring/whining noise (somewhat close to that a supercharger makes just not as loud).

It is still making that noise, but now it will sometimes make a nasty grinding noise when I put it in 1st after coming to a stop. The transmission just is not nearly as smooth as before either. The transmission had been flushed and refilled with GM synchromesh a month earlier, so I would rule that out. Also, at idle, you can hear a noise from the transmission, but it will go away when the clutch is depressed.

If anyone has any suggestions, please let me know, this car is becoming a huge headache. thanks