-It does idle high when I'm in neutral, but once I'm in in drive it idles perfect. Other than being really shaky.
High idle typically means a vacuum leak. Unmetered air is entering the intake area
-The power steering whines a lot and very loudly, I filled it up with new fluid and replaced the belt but those did not help.
The reservoir has a built-in filter that clogs over time. The whine and groan could be your steering pump being starved for fluid. Replace your reservoir and refill with A/T fluid.
-I'm not sure if this is just the cold weather, but it warms up very slowly. I believe its because the radiator fan is always on but i could be wrong. I`d leave it running for 15-20 minutes before leaving in the mornings and it would barely warm up at all.
Don't trust the gauge. Use an IR gun to confirm at the top and bottom of the radiator
-I've noticed that when it does warm up it runs a lot better but it feels like there are some performance issues. On takeoff it likes to go really slowly even with my foot to the floor then it suddenly picks up and goes.
Check that your Temp 2 sensor is in spec. Could also be a vacuum leak/unmetered air issue
-When i do try and give it a little gas trying to pick up speed or go up a steep hill it shakes really bad, and barely gets any faster.
Sounds as if it's not running on all cylinders. Check/replace your spark plug wire and ends. Have you had your injectors professionally cleaned? Consider it
-It still shifts pretty hard too, even after filling it with more transmission fluid and replacing the filter. Also it doesn't shift until i let off the gas unless it hits 4-5000 rpm.
Hard shift indicates a mis-adjustment of the transmission Bowden cable and /or vacuum leak. There is a vacuum line that travels from the brake booster area down the top of the torque tube to the transmission. Test the ability of that line to hold vacuum
-My windows, front wipers, sunroof, and brake lights don't always work. They used to work all the time but not rarely ever do. I'm getting 14-14.5 volts at the battery but if it sits for more than a day without being driven the battery is dead.
Have you cleaned your grounds? If not, clean them all. Have you cleaned the fuse connections at the Central Fuse Panel?
-My sunroof when its working will turn and open by hand but the little rubber piece that connects the motor to what turns to open it is ripped and I'm not sure how to find a new one or fix it some other way.
Why not just save this fix for another day? 
-lastly the rear wheel bearing needs to be replaced, I already have the parts i just need to know if there's anything different from any other car to look for or do when i change it.
This job can be a Bear without the proper tools. I just did this using a Sir Tools hub/wheel bearing tool made specifically for the 928 and it was not a lot of fun. The tolerances are very close on these cars. The freezer will be your friend.
If anyone can help me fix these problems that`d be great. Thanks for taking the time to read this. Oh and i forgot to mention the car is an `85 auto and I'm located in West Des Moines Iowa