Glad the problem is apparent. If your anything like me, finding a real problem rather then just throwing parts at something always makes me feel better, anyway, your questions
1. As long as the rust isnt on the bearing surface where it goes into the carrier or on the splines, shouldnt be an issue
2. Dont know what you mean by black mastic though, do you mean the neoprene seal? If your ordering parts anyway the seal is only 6 bucks, I would put it in to be sure anyway. If your refering to the black silicone, you will need to remove it from the transom and pump and clean the areas and apply new silicone to the pump just around the bailer and cooling hose fittings to seal them where there going thru the hull when installing.
3. If the black boot your refering to is the small one that goes between the pto and clamps on the driveshaft and spins with the engine, then its probably best you dont use regular hose clamps because the large worm screw can make the driveshaft a little off balance. The boot just holds grease in so I've heard of some people using zip-ties to hold it in place, when i pulled mine, I managed to keep the clamps from getting bent up
4. As long as you did not move the engine at all, ie loosen the mount bolts or anything, then you shouldnt need to re-align, but if you have never done it before, and your not certain its definitely straight, its not a bad thing to think about doing as mis-alignment can cause problems later on down the road.
5. When I pulled my pump last month, the driveshaft stayed in the ski too. Its no problem.
Good luck. Its relatively easy job to do. Just take your time. Any more problems, just post back.
Jeff