The coils are rated at a certain output and have X amount of resistance ect... may be possible the new coil is firing hotter or something but I really don't see how it could change spark timing at all. I've replaced a few coils and never really paid close attention to getting the exact size but do try to keep close to what the book states. Any way to find a used oem one on ebay ?
If you have a Yamaha service manual post up what the specs are for the oem version and also the one you have.
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