Not your standard gearing question.

I've got a buddy with a ZJ that keeps eating side gears on the Dana 35. I have come to the conclusion that either the housing is bent (unlikely as he dosn't wheel it) or, the carrier is tweaked. The question is if you replace the carrier reusing the same ring gear do you have to reset up the gears? We have come to the conclusion that if you have to do the set up process that is would be just a cheap to replace the whole axle. I know it's a ZJ but it's still a Dana 35.

Yes you have to re-shim it for gear mesh.

When I replaced the carrier in the 35 to install the detroit the only thing that had to be adjusted was the backlash.
Go to detroits webpage and look up the install instructions for a full carrier detroit, that would explain it.

If you need a carrier I've got one, it's a non -c clip carrier though. and the spiders have been robbed from it.
of course I do have another D35 that you could have the spiders from.
and about 6 spare shafts.

Who needs d35 parts?

If you are referring to the carrier bearings when you say side gears, then it may be that there are too many shims between the carrier and the case putting too much preload on the carrier bearings. There should be only enough shims to make a snug but not tight fit. Another possibility is the carrier bearing caps being loose causing the bearings to not ride square to the housing.