I have to go back to the parts catalogs lists. Rock Auto reflects the SAME CVs for both the Sport and the Tracker trucks.
Empire brand (new) LEFT side CV, part #805822 (for both model year trucks)
Empire brand (new) RIGHT side CV, part #805821 (for both model year trucks)
Surtrack brand RIGHT side CV, part # SK8020 (for both model trucks)
Beyond the air actuator in the 2nd gen diff, there is a difference in the width (to the side gears) between these two differential. That's why the inner axle shafts are of different lengths.
The difference, I maintain, is with the inner axle shaft. The 1st gen trucks had an inner axle shaft that was about 3/8ths of an inch shorter than the stock inner axle shaft of the 2nd gen trucks.
Therefore, IF they simply mounted your 5.12 gears onto your 2nd gen carrier, I think the problem you are experiencing is with the INNER axle shaft is too short now and may be pulling out of the side gear of the 2nd gen differential.
IF they had installed the complete 1st gen diff into your truck, then the inner axle would be of the correct length and you wouldn't be experiencing this issue.
So the EASY fix, I believe, is to drop your front axle housing, knock out the inner axle shaft that came with the 1st gen set-up, then replace it with the original inner axle, which will be 3/8ths inch longer.
OR... have them pull your front diff and, pull the ring gears off the 1st gen diff and have them set it back up the way you intended on the 1st gen diff carrier and retain the shorter inner axle shaft that came on the 1st gen trucks. This route would be more expensive.
You could pull the front diff, knock out the shorter inner axle shaft, pop in the new one and re-install the entire carrier in your drive way in about 2-3 hours of relatively slow work. That's IF your back is back into shape, captwoody. If your back is still giving you grief, then for sure, I'd have a shop do the work. I'd recommend having a second set of hands, even if your back was recouped 100%. The assembly is still heavy and awkward to remove.
That's my thoughts and I'm sticking to them. If your dash light comes on, then you at least have a solid air pressure in your actuator (no air leaks). They would not have had to completely disassemble your 2nd gen diff to install the 5.12 gears. They would have had to pull a side gear, unbolt the air actuator, then unbolt the ring gear and slide it off. Then slide the 5.12 ring gear on, bolt it down and reassemble diff and set the ring gear lash. Installing the pinion gear wouldn't involve disturbing the diff assembly any more than described above. Chances are pretty good they didn't screw up your front diff assembly and it is fine.
In the pic below, 1st gen inner axle on left, 2nd gen inner axle on the right.