I think all of the bearings and seals can be bought in a kit for about $80-90 total. I rebuilt the 3 speed in my 53 last year and she works great. My preference would be to lean toward replacing them. Youve got it apart and cleaned up, so why not?
I would guess the chip in the gear is on the first/reverse gear as that is the non-synchronized gear. When I tore into mine that gear was pretty beat up. It really didnt seem to effect it. I found another gear for cheap on ebay and replaced it.
Jeff