1. Clicking in the engine. It's intermittent while warming up and just sitting. HOWEVER when driving the ticking gets faster and slows down when the truck is slowing down. I'm assuming valves, but I thought I'd ask.
...could simply be lifters in the valve train.

2. There is rust bubbling on the passenger side lower corner on the windshield. Also a spot bubbling out of the windshield rubber near the middle. For me having owned Land Rovers, this can be more work than you want.
...I can cut the repair panel you need from a parts car. Depending on how bad yours is...more surgery than I know how to fix.

3. There are some older water stains on the ceiling trailing from the sunroof, which doesn't open however you can hear the motor running. The deal looks like it is dry rotting.
...It is common for the sunroof drains to clog up. There are numerous threads here that address sunroof woes and fixes.

4. Rear passenger window will roll down, but won't role up (this literally happened when I was looking at it). I took the panel off while looking at it, check the connections and switch. Also did this from the driver door switch since it wouldn't roll up from there either.
...with the windshield rust and clogged sunroof drains, this sounds like an ocean car. Probably corrosion in the motor winding. Swap motors.