SRAD 600 firing on two cyclinders Hellllpp!!

Hi guys my names Richy been biking for around 3 years have bought an SRAD 600 x reg (carbed) with the intention of saving it from the dreaded scrappy and was doing a good job until recently.
Before I bought the bike it had been sitting for 6 years so far I’ve replaced stator, battery, reg rectifier, sus bushes and bearings, swing arm, refurbed brakes, carb clean, TPS sensor, ECU, fork seals and various little bits. I actually got it through it’s mot as well without slipping the guy a few bucks.
but now she has decided to only fire on two cylinders 1 + 3 are not working. I have tried new ecu + TPS and change the plugs I have even tried switching the coils around but no luck.
Any advice guys I feel like my wages are going down the drain. My backgroud is working on compressors and used to work on cars as a Panel bearer so know how to work a multi meter etc.
Richy