If your crank is at TDC, and your valves on #1 are closed, and your rotor is 90 degrees out, it is a timing issue PERIOD. There is no guess work here. The rotor has to cause the #1 spark plug to fire while the piston is UP (near top) and the valves are both closed.

 

BTW, I'd also like to see a wet compression test on the #1 and #2 cylinders, to isolate whether it's valves or rings that caused the compression imbalance...but that's just for your knowledge. it won't keep it from starting either way.

 

I don't think timing is off, I would be real tempted to do a leakdown test though....... (need an air compressor for that particular trick.)

 

HOLY BRAINSTORM BATMAN!?!?
You stated that your distributor rotor is off by 90 degrees when the timing mark is TDC and both valves are closed. You should be either dead ***** on or 180 degrees off...not 90. I'll just bet that your distributor ***'y is loose, or was loose, spun outta position and your fuel timing is waaaay outta sync. Pull the dist cap back off, line up the rotor by turning the dist ***'y AROUND the stationary rotor to line everything up. You could still be 180 degrees out, but usually, the rotor should point to the 7 o'clock position (looking down on the rotor) with the #1 cylinder wire in range. Even if you're just in the ballpark, that should go miles towards setting your fuel sync to where the ECM will know to fire.
Then, leave the dist ***'y moderately loose and move her around your original mark while someone tries to start the motor. I'll bet your fuel sync is so "unsynced" it's not funny!!!

 

 

 

You don't. Timing is not adjustable on these trucks.

 

 

Custom tuning, sure. But, you need the right equipment/software to do that kind of thing.