Engine runs rough

At the moment, the engine runs really rough. It was putting out a dense grey smoke but this was because I had set the oil pump up WAY too rich. After setting it properly, the smoke levels returned to normal immediately.
It struggles to rev and huffs and puffs and misfires.
It appears to be running on both cylinders. But running really rough. It will not idle most of the time. Certainly not ride-able.

Initially I thought it was electrical. I pulled apart all the connector blocks and sprayed them with CRC and/or BrakeKleen and/or contact cleaner. I think I have probably done this to each connector block at least 3 times now. I also made sure that the battery was good and fully charged up. I could see spark at both spark plugs and both plugs were getting wet.

1) COILS, CAPS and PLUGS
I checked the resistance of the plug caps and it was zero, so I bought 2 new NGK caps/leads at NZ$42 each, with an inbuilt 5kOhm resistance.(NGK TB05EMA)
This made no difference.

Note that NGK plugs with "R" in their description (such as BR9ECM) means that the plug has an inbuilt 5kohm resistance. I am not too sure if you are supposed to use a 5kohm lead with a 5kohm plug, but that is what I am doing until I learn otherwise. NGK link.

I checked the resistances at the coils and they were zero across the terminals and about 3.3kOhm to lead end.
This gives a total resistance of 3.3k + 5k in the cap = 8.3k.
I know that 3.3kOhm seems a bit low across the HT coil, but a friends bike that was running sweetly measured the same.
I even swapped coils/caps with him, and still no difference.
I got a new set of NGK BR9ES plugs at $8 each and tried them. No difference. (The BR9ECM's were $25 each; I ordered 2 but then the bike shop rang back later and said that they would rather not get them in as they would have to buy a box of 10 and they didn't want to have 8 plugs sitting in the warehouse for ever. Welcome to New Zealand.
I set the plug gaps to 0.6mm
I also checked that the grounding of the earth wires on the wiring loom was good.
I unwrapped the front 2/3rds of the wiring loom and checked that it was all OK.

2) PGM II
I put my PGM on my friends bike and it ran OK. So I guess My PGM is OK

3) TPS
I measured the resistance across the Throttle Position Sensor (both ways) and made sure it made sense.
It varied from around 3kOhm to 5 kOhm from memory.
The power valve drive motor behaves properly with TPS connected and disconnected

4) PICK UPS
I fitted the flywheel pickups and wires from my spare engine. No difference.
I checked that the flywheel was on properly and couldn't float around on the crank giving bad timing signals.

So then I thought, well maybe it is carburation:

5) CARBURETTORS
I fitted a set of carbies from a friends bike that was running OK. No difference.
Both his and my carbs are set to standard settings with slightly different needles BPJ/K instead of BPG/H) and his float level was set to 16mm instead of 13mm.

???)  I am at a loss to explain why it doesn't run properly.
A) Maybe I have made a mistake during engine assembly, but I can't think what.
B) There is no little tacho wiring loom in place, but I seriously doubt that not having the tacho wired up would cause any problems. I actually just disconnected it on my friends bike and it did not affect how it runs.
C) Maybe there is some random problem in the rear part of the wiring loom?
D) I will check the compression on both cylinders tomorrow, just in case that sheds any light on this problem. It feels like good compression with the kick start.
E) I guess it could be a leaky centre main bearing seal, but this is brand new, so seems unlikely. But I guess I will have to do a crankcase pressure test the way things are going.
F) I am running V-Force III reed blocks. I doubt these are the cause of any problems?
G) I am running single ring Wossner RM125 pistons. They have a shorter skirt, but still block the exhaust port entirely at Top Dead Centre.

It is really quite frustrating to have such an elusive problem right at the end of the complete rebuild of this bike. But I guess this can be viewed as perfectly normal?