If I may?
From reading the first post, it sounds to me as if two things were done: 1) Rebuild of the front axle and 2) Installation of new gears in both 3rds. Nothing else if I read correctly. So, the front pinion should be in almost EXCATLY the same place, in relation to the drive shaft, as it was before all this work. The issue is noise and vibration, most probably not related to either drive shaft or the transfer case, assuming installation of the two thirds was done correctly and the front axle re-assembly was also done correctly.
I did mostly gear changes during the 10 years I owned my shop (in the Dallas area) and used Nitro for the last four or so of those 10 years. Prior to that, I was a professional tech for almost 20 years, with the last dealership position at a Lexus franchise in Dallas.
I think your setup is faulty. Nitro gears are generally easy to set up and I naver had any issues with break in. Your break in procedure sounds exactly like what I used to tell my customers to follow, which worked for me.
The only other issue I can imagine is a physical interference between the substantially thicker new ring gear and something in the housing, not unheard of.
Re. the leaking rear pinion: Nitro uses an aftermarket seal in their install kits that bit me a couple of times. I got to where I would keep OEM seals around and pass on Nitro's part.
Feel free to e-mail me,
offroadwine@yahoo.com I check personal e-mails a lot more frequently than I can get on Mud.