If I understand you right, you just want to remove the cans, keeping the rest of the exhaust system in place? In that case, I don't think you're gonna hurt the engine, but it's probably gonna affect your tuning, for better or for worse. I'll be running a Murray sidewinder, no baffles, but it'll be tuned to produce the powerband useful for 1/4 mile drags. I won't be riding it on the street though...