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If you have the SE or other high perf. aftermarket air cleaner/breather, you should be fine. The stage 1 flash is designed for the SE ac kit with stock exhaust. If you have the stock ac, you might be a little rich. I've run the stock mufflers with the SE ac/breather/flash and on my '04 Road Glide and it ran perfectly.
If you still have the stock ac/breather, you could always just put your stock mufflers back on and see how it runs. It shouldn't hurt anything and if you are running too rich, then have it flashed back to stock.
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