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1997 speedster backfiring

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cdmiller2

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I am having a backfiring issue as soon as I try and start the right motor. I have tried replacing/switching the following:
stator
voltage regulator
coil
plug wires
plug boots
spark plugs
carbs (freshly rebuilt)
eliminated fuel selectors
new fuel lines

The odd thing is when you switch the ignition plug and the plug wires to the other engine it runs as normal and does not backfire. The engine that does backfire is a brand new sbt rebuild, with a new rotary valve that is timed perfectly. Any help is greatly appreciated
 
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