It's not hard to set up 8.25 gears if the pinion depth is set right. You really don't need any special tools to set backlash/ preload. If you take your time you can set them up with a screwdriver by taping on the spanner holes. Try pattern first. Since pinion depth is unknown, see if you can get a good pattern, if nothing else, you will know what else needs adjusting. Getting it driveable is just backlash.
There are a couple of things bothering me though. The cap "backed out"? Does that mean the bearing caps are loose, because, when those bearing caps are tight, the adjusters don't move. Also, there are safety clips which latch into the adjuster spanner holes and bolt to the bearing caps. Are they missing?
I certainly would not drive it in it's current condition. Yah, I realize the shop messed up, but they will probably only be culpable for the labor, not the gears if you supplied the gears.
Oh, and check the front. If they hosed the back, who knows what they did to the front.
Good Luck!
Ron