I would ditch the manual hub, there is no point of going out of your truck to lock into 4x4. You have shift motor that electronically shift into 4wd for you. I am not familiar with the setup, so I won't be much help. As for water leaking from the rear window. It is not the window that is...
I got mine from Ebay, with lots of caution. If you decided to get it, make sure it is "Hub Centric". This is where the wheel will rest on the center of the hub and not the studs.
Hummm.. I'll take that challenge. Free foods for life (just kidding). I've mentioned to a few posts and noticed you've replaced the spark plugs. You might want to replace the plugs with MOTORCRAFT plugs. Its seem like these engine doesn't do well with anything but their own. If you do buy...
Try shifting it to 4th gear when engine is off. If it shifted smoothly with engine off, I would go with damaged synchro. I have a buddy who rebuilt manual transmission, but he is in Fresno, CA.
Have leaking oil dripping in front of the engine? I would look into the connector to the crank sensor, the connection may have cause your random issue..
Those stop leak are bad news... It will clog up the pores and your heater core. Although, if it doesn't do any harm. I would just drive it. If you replace new radiator, new hoses (upper and lower) will need to be replace as well as thermostat and/or new heater core. This will get pretty pricy..
The upper springs are suppose to keep the brake pads down and not make rattling noises. If it is rubbing, you may want to make sure it is seated properly. It shouldn't cause any rubbing.
Go with MOTORCRAFT SP 500, you will be just fine. Oh, DO NOT BUY THOSE OF EBAY OR AMAZON, they are not original MOTORCRAFT (fake). Get it locally, where you can get 2 years warranty.
I used to use whatever oil I could get my hand on (cheap) on the ole days. Now with newer modern engine, its best to stay with whatever the manufacture recommends on your oil cap.
Does the engine crank? If not, I would try to by pass the "clutch pedal" switch and see if it turn over. Noticed the starter relay and solenoid are replaced, make sure the wires are connect to the original position..
Never heard of it locked up, but soft and mushy. There is a Neutral safety assembly may have block the push rod from pushing down on the master cylinder.
Clean or replace the "IDLER AIR CONTROL" (on top of the throttle body), and MASS AIR FLOW METER (after the air filter box). Spark plugs are good? Motorcraft seem to be the only choice, when replacing the plugs.