You have alot of stuff going on at once here. You have given us 2 important clues. 1) fire out intake 2) low compression
The most important step in trouble shooting an engine problem like this is confirming the mechanical parts of the engine are correct. I am going to assume you have not removed the camshafts since the engine was running last. If you did have the camshafts out the engine you must confirm they are timed correctly and you have proper valve clearance.
Next comes compression and leak down tests. You already did the compression test, it says you have a problem. First was the compression test done correctly? Does the manual specify open or closed throttle? Did you measure it the way the manual specified (open or closed throttle). Confirm this.
Next, is the compression gauge a known good working gauge (has it given good results on a known good engine). Compression gauges have a check valve in them some times they leak and give bad readings. if you are confident in your gauge and your test method you have a compression problem. You state there is fire coming out the intake, so I am going to assume your blue rags are not stuck in the intake tract giving you bad compression readings.
A leak down test needs to be done to determine where your cylinder leakage is. This test will show you if you are leaking
past your intake valves (possible, you have flame blowing into your intake port), exhaust valves or rings.
Incorrect cam timing can also cause low compression but on an DOHC shim under bucket engine if your cam timing is off by much you will likely have bent valves and that will show up in the compression test and the leak down test. In fact, if given only this information, low compression on both cylinders and fire out the intake, my first guess would be the cams are timed wrong and you have bent intake valves, but if you never had the cams out of the engine this is very unlikely.
Don't spend any more time or money on ECUs, wire harnesses and sensors until you can explain the low compression.
Don't use starting fluid on the engine, it accomplishes absolutely nothing. There is something wrong, identify, fix it and the engine will fire up instantly.
Is it possible, while you were working on it, something fell in the intake tracts and made its way into the cylinder and caused piston/valve damage? This does seem like a stretch since both cylinders are low on compression.
Some of this advice may seem very basic, but I am not sure of what you have and have not done. If any of it helps great, if not ignore. Good luck.