Well the bike was designed to run properly n the BR9ECM's, and if it isn't then I'd personally try to find out why rather than change something else to correct the bad running.

Maybe it's got an 'interesting' tune, maybe the compression is low, maybe the power jets are blocked and the mains massive to compensate, maybe the coils aren't good or the cable connections dirty, maybe it has a partly blocked fuel filter...

Dunno, but unless you find out what's what with the state of tune then I'd suggest setting everything back to standard.

But that's just me!
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