Yesterday I opened up my transmission to replace what I believe to be a bad Input shaft bearing. I also went ahead and replaced the mainshaft bearing while i was inside. I'd like to ask a few questions before i seal it up so hopefully I don't open it up for a long time.
First: I understand the transmission should be kept clean and from reading a few transmission rebuild articles I'm lead to believe that using brake parts cleaner or similar solvent is acceptable. Is this indeed true?
Second: I rotated the differential and it makes a rather loud whirring noise and also has what seem like "hard spots" in its rotation. It doesn't appear to be damaged at all but I really have no idea. Can someone describe what normal differential assembly should look/feel like?

 

Brake cleaner is fine for cleanig the parts. After the bearings are clean, lube them with some MTF and spin them. If they are noisey or crunchy feeling, they need to be replaced.

 

Clean the main and counter shafts out as well.

 

strip and clean the shafts as little bits of debris from the ISB going bad will clog the oil ports.

Just bought a 20 gallon parts cleaner tank to assist in doing this!