I would start by looking for and air leak someplace. Did you do a leak down test to make sure the crank seals really are OK, even if new. Check that the carb boots are not leaking as well.
Did you set the mixture screw on carbs, does bike respond to a change in mixture screw adjustment, if it's not responding, that's sign that air getting in someplace else, or pilot jet clogged, but you said you cleaned them, so air leak possible.
How about the rate of fuel coming from gas tank, make sure it flows good. Check that screen isn't clogged causing fuel to just dribble into carbs. You did say you changed tap, but it's easy enough to confirm fuel is actually flowing good.
No harm in checking the ignition, but it's probably the least likely cause if bike is running to 6k rpm. If you have a timing light you could put it on there to confirm ignition is firing when you Rev it.
I would not draw any conclusions from the plugs until you have it fully running. If you are using oil injection, the oil is getting in there regardless of what's going on and could mislead you a bit.
Keep a close eye on the temp as you are running it. If you have an IR temp Guage (point and shoot) you should measure the temps of each cylinder at the exhaust pipe near head. Both cylinders should be fairly close in temp after bike is warmed up. If one pipe significantly hotter, that is gonna be the one running lean. But don't be tricked cause if both cylinders close in temp they could both be lean.
It might take some time, but you will get it sorted. And you'll feel good when you do.
