Definitely replace the bearings. First off, you're high-mileage so the bearings are without question half-way through their practical lifespan...even if the diff was in perfect condition. Second, you have driven 100 miles with the Cuisinart running...grinding small pieces of teeth into "tooth dust" and marring the bearing surfaces. Third, its sometimes impossible to remove and re-install the pinion bearings without destroying them. So...NEW case, NEW r&p, NEW bearings, NEW seals, etc. That's the right way to do it. If you plan to re-use your open carrier, make sure to give it a good cleaning and check for spider damage.
Looking back at that diagram: You can junk items #31, #32, #33 (crush sleeve, pinion bearing, pinion shim)....just leave em on the old pinion and display it on the "carnage shelf" in your garage. All of these will be replaced with new parts but, some guys like to pull the pinion shims out and use them to achieve a starting point for the new set-up. You might also include #48 & #52 (carrier shims) in your package to the set-up guy. The axle guys I know have boxes full of Dana, 12-bolt, and Ford shims but, since you got somewhat of an odd-ball build...including your old AAM-7 shims might be helpful to the the set-up guy.
The only items you need to salvage from the pinion are #1, #2, #3 (yoke, nut, and washer). These will get transferred to the new pinion. You might also need #7 (vent) and #53 (plug)...not sure if those come on the new cast-iron pumpkin. This is all standard axle rebuild stuff...the only exception being item #57 (half-shaft bearing), which is somewhat special for this IFS application. You'll probably want to install a new one in the side of the c.i. case. There is a similar roller #12 on the outboard end of the housing coupler #13 but, it is somewhat isolated from the shrapnel so you can probably leave it alone.
Those "cracks" in the aluminum are there on all AAM-7s. However, I don't think they are cracks...probably just a result of the casting process. I believe these cases may be "pressure cast", which might cause the strange appearance. If you look at them under a microscope you can still see traces of Dr. Pepper and Sprite cans.