Start with the basics Jag,
pull the plugs out and have a good look at them. If you've got a white/blistered plug it's running too lean on that pot and it could be either fueling or a leaking exhuast gasket if you've got a real sooty or a wet inky one it's most likely electrical.
You can just disconnect the power commander and it will go back to the original fueling from Honda but I don't think that will be the problem unless the map is way off.
When was the last time it was serviced? plugs wear out and shims get too tight, all things need to be taken into consideration.
If you got any more details I'll take another stab if you like
Pete.l
P.S if the carbs have been off I'd leave them that way. The fuel injection works better without them
