so the manual AHU 98 tdi jetta has some serious flaws but not that they cant be fixed (for a 25 yo car) of todays standards.
So before i dig into your list, here is my (or just the forums) recommended list for your car.
before you drive it much if any more, you want to do the timing belt, its only good for 5 years or 80K miles AT MOST and anything more is a ticking time bomb. not to say that they cant go further but there is a very high risk to little reward here.
CHANGE YOUR TIMING BELT and get up to date on all your fluids, ALL OF THEM including the brake fluid!
ok so now that i got that out of the way,
Your AC issue might be related to your temp gauge. (solution: replace coolant temp sender on the radiator right in front of the power steering res) this might fix your AC. this is a part of the AC for the fans but not the clutch
The AC has a few items that wont let the clutch work, the high/low pressure switch on the dryer is the key if everything else like fuses and switches are ok.
Try jumping it and testing it with a multimeter, same with the ambient air temp under the front cowling somewhat next to the windshield wiper motor area.
If you go and find out that all the electrics are working properly, its then time to get a set of gauges from harbor freight.
Now as for shifting, there are about 5 items that make this a PITA because old car and worn parts from dumb engineering standpoints.
1st on the list i would say is the shift tower, there is a plastic bit that holds the lines, plastic bits that the lines have on them that go to the other platic bits, another plastic bit that probably is gone by now that rids the tower rail. there is also more plastic bits here and there for the shifting inside and you have to lower the exhaust to get to it. You can adjust things but chances are your O2J shift tower is garbage and the tower bearing and the shift position ball bearing thing is trashed. Solution, trans swap or shift tower swap and or change the trans fluid.
the way to find out whats good and whats bad.... anything with play in it under the hood on that shifting tower, is BAD. a good tower and all its connecting bits is stiff and no play, or less than 0.25mm worth.
