I had a 99 Dually on 35's with a 4.10 D80 and swapped the carrier and r&p to a 3.54 in the 4.10 existing housing. I encounter ABS and computer headaches. Granted this was a VP truck with 4 wheel abs so you shouldn't have computer issues. BUT the placement in the housing for the abs or wheel speed sensor did not position the sensor directly above the abs tone ring with the new 3.54 carrier which I believe caused the abs issues. I assumed all of the D80 housings had the same location for the abs or wheel speed sensor. They may, but I had issues. The difference was roughly 3/8-1/2" offset from the sensor and abs tone ring. Hindsight, I would have just swapped the entire housing for one that came with a 3.54 gear. I think you will be much happier with the 4.10's on a 35"+ tire. If the truck is only a rear wheel abs truck, the housing may make no difference because there are not front wheel speed sensors to compare against the rear speed sensor. It is also much cheaper to swap rearends or buy a complete one than to buy new D80 carrier, R&P, AND have it set up.
Not to hijack but if anyone can confirm the 3.54 and 4.10 housings have the exact wheel speed or abs sensor location please advise. It will give me some insight on the quality of shop work that set up the rearend.
Sorry for the long post, just hope others don't go through that headache. I vote 4.10's.