Good News, replaced both the front main-shaft and front counter-shaft bearings which solved my grinding problems! So, to recap the project, I am finished installing a 82 280zx transmission, r200 3.9 rear diff, and a new clutch disk and pp.
Bad news is that I now have a shudder and a howl noise. The shudder happens when accelerating from a stop. It feels like the diff is grinding/not catching. It seems like the problem does not occur when I keep the revs high when accelerating from a stop. Does not happen in any gear besides 1st. It might just be a user error with me not being used to the new clutch/tranny. I've read that adding some friction modifier helps with this issue in LSD's, but IK this is an open diff. Could that help here? The howling noise I'm pretty sure is transmission related, as it only occurs in 1-3rd gears. It does seem to follow the rpms and go up when accelerating, but disappears in 4th. It is not that loud to begin with though.