So i got her to run on all 4 cylinders and... the Culprit was the speed and reference sensor gap the whole time! I never re-gapped it after the rebuild since i had left the bracket in the same position but it must have moved somewhere along the way. Yesterday, I did testing after a long day of work and to my embarrassment, gapped the wrong sensor. The thump i got when pushing the bracket down when re-gapping was just the pivot screw bottoming out on the bracket so i ruined the speed sensor. However, it did run on 4 cylinders, backfired a few times or missed so i shut her down and realized my mistake afterwards. The tach was also now properly reporting engine speed!
All in all, it seems a Larger-than-spec gap was causing improper ignition timing from the start. It's amazing as you can almost tune the timing by loosening the screws and tightening them down on the sensors as well. It was cool to see that testing too before i realized my mistake. I heard a horrible screaching sound and pulled the sensor closest to the front of the engine (thinking this was the speed sensor at the time) to see it was perfectly fine so i assumed the other one was too (I was wrong

). So im going to order a new sensor and be more competent this time but for anyone having this same issue or may be in the future, I'd like to wrap a few points here.
Engine Running on 1 & 4 cylinders only:
Ignition:
-Check spark plug tips for oil or carbon buildup.
-Check plug wires for resistance as-well as any dropouts when bending the wires.
-Check for corrosion on distributor cap and rotor.
-Identify DME grounds behind the engine and make sure they are connected.
-Check continuity of Speed/Ref signal to back of DME harness aswell as continuity between pins
-Check for proper sensor resistance on: Speed/Ref sensors, DME temp sensor, AFM & TPS.
Oscilloscope testing:
-Check for proper waveform shape (Sawtooth) and P-P voltage on Reference sensor of 2.5 volts
-Check for proper waveform shape (Sinusoidal) and P-P voltage on Speed sensor greater than 2 volts
-Check ignition pulse signal for proper timing between pulses for idle (33.3 ms between pulses = 900RPM)
Fuel:
-Make sure you have 1/4 Tank at minimum
-Change fuel filter
-Check for fuel injector leak down or operation using a fuel pressure gauge
-Check for fuel rail leak down using Fuel pressure gauge (Attributed to faulty FPR or dirty Check valve)
-Check for proper fuel pressure when cranking, running and 20 minute leak down. (Clarks garage testing)
Compression:
-Check for even compression across the board
-Check for Oil in coolant or vice versa
-Check piston heads with a cheap cell phone endoscope (Anykit $30) and check out condition on piston heads
Thank you everyone for you help, I wouldn't have gotten this far without all of you. This community has been such a great place to browse and find like minded people who love to tackle problems and solve them in any way possible. Excited to show you all what she'll become in the next few months!