You are running to the parts store, so I'm going to reiterate some of the chat stuff here to keep people up to speed.
You said you think the lifters are over pumping or somehow the valves are being held open. Currently you have the timing cover off to verify timing. You definately have a key on that camshaft, right? You definately engaged the HB on the key before tightening?
The rockers are stamped 1.6 on them. That's good. Hopefully they aren't the adjustable ones, either way..shouldn't have enough to cause this issue.
To try and verify if the valves are open and bleeding off compression, I would do this. You have the timing cover off. Turn to TDC (likely you already are there. Put your air hose to the cylinder and add air like you are holding up the valves. If you hear excessive leakage, then something is up with your valve timing etc. This to me is the true test of your theory on low compression.
You say you have spark and you have 50psi of fuel pressure with key on. Thing here is.. your plugs are coming out dry. Ensure your fuel injector fuse is good. I've had this fuse blow before. Not sure if you changed injectors etc during the build/rebuild. Definately something to check with the electrical situation you have now with that trans swapped and some circuits no longer being used/extra wires laying around. Easy test here, take a vacuum line and stuff it to the port under the snout on the lim. Hit it with some brake clean etc.. you understand and try to start it.. if you get something..then it's injectors/maf. Maf can also put PW down so low that it won't start.
Lastly.. check your ICM connector. If that puppy is loose.. it can cause no start.
