Whose c-clip eliminator kit are you using? Also, which disc-brake setup are you using? What is this "disc brake upgrade" supposed to do, exactly?
C-clip eliminators can usually be used with factory-based disc brake setups without having to buy anything else, but maybe a little fitment (machining) work to the housing and/or caliper brackets. I've only dealt w/ the Moser c-clip eliminator kits, but they sure as hell don't need the axles to be machined down to fit the bearings. That would ruin a perfectly good set of axles.
You can run whatever differential you want w/ c-clip eliminators. The axles will mesh w/ the splines of the diff to turn the wheels, but it will no longer be the responsibility of the diff to hold the axles in at the inner ends, since the bearings (in the c-clip eliminators) pressed onto the axles will hold them in the housing. As far as whether or not the mini-spool will work w/ the factory track-lock, call the manufacturer when you have a little time to hold for their tech line and get a straight answer. You're obviously not getting any good info from Jeg's.
Finally, and I mean this to be as constructive as possible, why are you running rear discs on a car that gets most of its mileage in quarters? Drum brakes are lighter, and reduce complications w/ c-clip eliminators. I would suggest going back to the old school. Hell, I'll sell you my stock drum setup dirt cheap if you want it, the 5-lug drums are easy to find.