I have a couple questions about your setup and axle you bought since I'm about buy the axle from MSA.
Did you center your diff cover from the back with the pinion flange offset or did you center your pinion flange in line with the driveshaft and your diff cover offset?
Do you happen to have the exact length of the shafts you bought and what did MSA have to say about your problems?
I'm no expert on CV's but I would think they be setup to have enough travel for normal driving squat(full compression) and full droop. I could see them fully expanding and maxing out the CV boots but still held place by large C clips the clips and keeping them from popping out when Jacked up on stands.
I just don't understand how MSA would not have warned about this little problem. Thanks