sr20 in s14 transmission dust boot issue

[Catch240]

Ok. So I recently installed a redtop sr into my s14. I forgot to remove the dust boot from either the driveshaft or transmission. I drove the car with them still on for about 2.5 miles before I figured out what was going on and headed back home. I removed the dust boot on the trans and the dust cover on the driveshaft.

My problem is that I am still having a grinding/screeching noise coming from the rear section of the trans, where the slip yoke fits up. Im wondering if anybody else has had this problem.

Im wondering if I ruined something in the tailsection of the transmission or if the problem could be the driveshaft going bad. A lot of heat was cause from the two dust covers rubbing.

thanks for any help. I did search just couldnt find anybody with the exact problem.