That's not much regarding all you've brilliantly done already. Just a last inconvenience before the back to road step.
Jugg O'H boy how i feel for you after all that work. Any chance of getting it welded. And we all have done the same at one time or another. I built an a65 engine and forgot the crank shim washer. Luckily i didn't do to much damage but just goes to show you we are all human and we do err sometimes. I know this is of no comfort but i do feel for you. Joe.
Jugg, Don't give up now. We all want to see your project finished and back on the road in fine fettle
Have you identified which cylinder is dead? (check which exhaust manifold pipe stays cold after running the engine). I would then start by checking that cylinder's coil connector and check that the coil is pushed fully home. You could also swap coils around to see if the problem moves to another cylinder, in which case it could be a dodgy coil. If no further forward then start looking at the injectors and swap them around. I assume all 3 sparkplugs are good?
Is the MIL (malfunction indicator light) on after starting? If you have access to diagnostic software you could check for fault codes. I would also check that the 3 rubber hoses are all properly connected to each throttle body.
It might be worth checking the connectors to the ECU? Have these been disconnected at all during your rebuild?
If the injector checks out ok it might be an idea to look at the crankshaft position sensor and toothed wheel rotor. Check the rotor for any damage to the teeth and make sure it is clean. The air gap should be ok as it is firing on 2 cylinders but it might be worth checking anyway. Does your bike also have the camshaft position sensor in the cam cover? Apparently this was omitted on later models.