Drive shaft was removed before and at the wheel side not been protected, still has grease but no doubt picked up some debris, what's the best thing to clean out with? Do these need packing with grease prior to new shaft being installed?
I'd scrape the bigger chunks out with a screwdriver and then just clean it up with a rag and degreaser. No need to grease it, the CV joint is the side that should be packed with moly grease.
As above. Run an M8 tap down the threads of the output flange and try and clean as much rust (all of it haha) off the cv mating surface as you can. Wire wheel or similar... Doing that gives the bolted on joint as much chance as possible of not coming loose