Transmission bearing?

[ncturbospecv]

I recently replaced my transmission with another used one due to terrible grinding issues and bad bearings(found the bearings on my drain plug). When doing this I put in a new comp stage 4 clutch, throw out bearing, and pilot bushing along with resurfacing the flywheel. The "new" transmission I put in the car is acting up making a slight grinding noise when letting out the clutch. I pulled it out and put in new OEM throw out bearing and oem pilot bushing as to thinking that was the issue. The pilot pushing I pulled out (one i installed with the new trans/clutch) was reamed out slightly bigger like the input shaft wasnt staying straight if that makes any sense. With the new oem parts installed the transmission is still having the same issue making a grinding/rattling noise when letting out the clutch. My question is could it be the input shaft main bearing causing this? Should there be any play in the input shaft at all?

To add:
The trans makes no whining noise with the clutch engaged while idling or driving. Before replacing the new throw out bearing and pilot bushing the car was making a terrible grinding noise with the clutch pedal pushed in and free reving the car. It seems to be fine untill you warm the car up and then it starts to make the grinding noise while letting out the clutch.