Make sure you are 1000% the system is grounded properly. I recently dual sported my bike and it was running similarly to like you describe. I could not give it more than 1/2 throttle without it breaking up. I went back over my wiring with a fine tooth comb and found the bad ground. My bike rips again.
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-Mike
2009 Beta Evo 300 4T - 1982 Suzuki PE175
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