Yeah, customs housings are the key. Stock housings have issues with the pinion bearings supports, mostly the inner support. A lot of the broken 9" axles i've seen were caused by pinion issues. Custom housing beef up the inner pinion support a lot... But they are a strong axle, which comes from the pinion being so low on the ring gear.
Seems like the 8.8 is just a better choice, they are cheap and plentiful, 95+ come with disk brakes, 31 spline axles, almost perfect Jeep width... The only real downfall i've seen with them is they like to spin axle tubes, but that is a very easy fix.
I had the horrible D35 for a few years in my TJ, for a while it was even aussie locked on 33s and it held up fine. I had a friend on 36's that broke shafts on a regular basis. I did a bunch of research on what to replace my 35 with and the 8.8 just came out on top for me. A Jeep 8.25 or D44 was just to expensive and not worth the swap. I picked up a 4.10 geared 8.8 for $175, and spend another $300 getting TJ brackets put on...