transmission question...

I have a 88 chevy 3500 dually and I had the transmission and clutch replaced when I got it about 2 years ago. Before the trans was replace and afterward it makes a rattling noise that comes up the shifter. Do you know what that is and how it can be fixed? The transmission the the step below the rockcrusher version.
Also it has rust below both doors the biggest hole is 3' by 5' how much would that be to fix and or can bondo fix that big of a hole?

Thanks.

when the tranny was replaed did the repalce the pilot bearing. if not then the noise is the input shaft of the tranny rattling in the worn pilot bearing. bondo will not fill in a 3 inch hole, pop rivet or weld in a piece of metal on then use bondo.