Boy that's a lot of things to cover in one post. Many of those issues have been addressed here before, so you can do a search for them.
1. If the fan seems anemic, it may be because of a failed vacuum pod or pushbutton control unit misdirecting the airflow. Check for air coming out the defroster vents or the heater ducts.
Yes, it sounds like the auxilliary fan is not coming on. Spin it by hand to see if it turns freely.
2. Can't help you there.
3. The old Bilsteins will be great. No worries there. The continued bouncy rear end is probably the accumulators. Search for that word here.
The seat covers can be moved yourself if you're patient and careful. Thomas Pindelski's web site probably tells how to do it. If not, I'm sure it's been written about somewhere here on Mercedesshop.
4. That's not the differential leaking. It's the CV joint. You replace the entire half shaft, as the CV joint inside the rubber boot on each end is integral with the shaft. Not too big of a job. Search here for half shaft, axle shaft, CV boot, that sort of thing. There are two different types of these, so the ones from the parts car may not fit. Check by removing the bolt from the center of a rear hub on each car and comparing their sizes.
5. A pull when braking is not likely to be caused by tires. This bears further investigation.
6. Can't help you there. My only JB Weld experience was a failure, but it was an inappropriate application anyway. Others have had much success.
7. The original radio had all the speakers wired through a fader control on the console. If the radio was replaced, the P.O. may have bypassed that connection. Look for wires in the console that are hanging loose.
The antenna may need to be lubricated, or the mast may be bent, or the nylon part may be missing some teeth. Lots of good info here on antennas if you search.
8. Sorry, I never owned a wagon.
9. Yippee!
10. The transmission fluid cooler that is integral with the radiator makes it easier for the tranny. Drive and enjoy.