Transmission Noise?

So, after starting my car (mostly when cold), something makes a metal-on-metal grinding noise while it up-shifts. This is especially prevalent under heavy acceleration. I noted that the trans had a small block dust cover, (The transmission is a 727 TorqueFlite mated to a 383 BB). The old dust cover was eaten up, (it showed signs of striking the flex plate), and we replaced with the correct BB cover. It still makes noise. After shifting to third, the noise is gone, and does not happen again until restarting (Starter related?). Any ideas would be appreciated.
Author: The Horvaths