Everything is repairable, or able to be modified.
Front windows:
There's three little bushings in the motor, they are dried up and brittle. You can rebuild the motor with these bushings, but you have to modify the bushings to fit properly. It is worth the time as it cost 20 dollars for both sides or 65 dollars for one window motor.
Rear windows:
They could be upgraded to the 95-01 track and regulator, versus the current cable driven system. This does require some modification and time, but nice in the end.
Exhaust:
Since it is missing, you could upgrade it with an aftermarket muffler of your choice. There's cat back systems available, they just aren't MY particular style.
Automatic transmissions:
It needs fresh clean filter/fluid/extra coolers to stay alive.
Automatic hubs:
They tend to not work when needed, and worthy of doing a manual hub upgrade. Rebuilding the auto hubs is just a failure waiting to happen again.
Electric transfer case:
This has a plastic stop for the motor, that may or may not be broken and CAN cause the transfer case to not work properly.
Engine:
After 200k miles (sometimes sooner) head gaskets or cracked heads (usually both) cause over heating problems and driveability issues. This is resolved by purchasing brand new aftermarket cylinder heads. The aftermarket heads are better designed.
Routine maintenance:
Basic normal maintenance goes a long way with these trucks. It is worth the extra money to buy motorcraft spark plugs, and wires if you can find them. A good quality oil and filter works. Belt, hoses (including heater hoses), antifreeze are recommended to be changed due to not knowing the history of service. Water pump and thermostat should be serviced as well.
A wise mechanic told me "the secret to a long living 4.0 v6, is to not let it get hot."
If you use google for a search and put explorer forum in the search it will find posts on here. I prefer this method, as the search feature on here is hit or miss.