Need a little help with my bike.

Could be a coil, injector, or any related wiring causing your described problem. I would try to isolate the problem cylinder by disconnecting injectors one by one. Once you have determined the cylinder, swap the coil with one from a good cyl. If the problem moves to the other cyl you've found the culprit. If it doesn't move try the same technique on the injector. If you still have the problem on the same cyl you'll have start looking at the wiring.
Also may try to shoot a temp gun on the exhaust manifold tubes while it's misfiring if possible and compare readings of all 4 cylinders to find the culprit.
 
As you said it clears out up high, so I would skip swapping the secondary injectors, and only swap primary injectors. Also check for air leaks by spraying something around the intakes between the throttle body and head.

It makes perfect sense that the primary injectors are the biggest pain to get too...such is life.
 
I'm going to check the coils when I get home by moving them around. I also found all the parts I need to rebuild the fuel injectors and since it is 10 years old and already mostly disassembled I'll go ahead and do that.

I can't see it being a air leak since that would cause it to lean out more @ high rpm then low rpms and the problem is only at the low.

New injectors would be $115 a peice and a new ECU is $800. Hopefully its just a coil which is a $50 piece. It'll only cost $80 to replace the seals on all 8 injectors. I'll let y'all know how it goes.
 
Has the bike sat for extended periods of time? Have you taken the fuel pump out and checked the fuel filter? It very well could be a semi-clogged injector.

You can check to see if there is an air leak around the throttle bodies by spraying some starting fluid. If the idle goes back to normal, there is a leak there.

It really does sound like some sort of a fuel issue. The charging system souldn't cause the bike to have a rough idle at low RPMs and smooth out in the higher RPM's.
 
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Check the simple stuff first. Safety switches have a funny way of masquerading as running issues. Seen a side stand safety switch give a hesitation and stutter because it was failing and the vibes at a particular and lower rpm made the switch engage ever so slightly and it came out as a running issue of course. Check connectors and wiring.
After that I'd go to all secondary fuel injection. Honda did have a slight issue with their AIP sensors in the past so go through all of them and check with the dealer about service bulletins
 
just something to look at, but the petcock fuel filters and the inline fuel filter if you have one installed. Make sure they are clean.
 
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