So are there different types of re-flashes? Can my '09 M1100 have it's ecu flashed different ways?
The short answer is yes. Though put simply, there's only one ideal fuelling map for whatever intake/exhaust setup you arrive at.
But there are as many mapping variations as there are intake and exhaust combos, mine will be different to yours. Mine has the rev limiter raised to 9,500rpm, others prefer to wring it out to 10,500rpm.... the permutations are almost endless.
I am definitely going to try the MWR kit and the ECU reflash. However, I will keep my stock exhaust as I cannot afford the Termis. I assume I can just remove the flap? Are there DB killers in the stock exhaust I could remove? and would it make any difference?
On M1100/M1100s the easiest and least costly way to make the exhaust flapper gate go away is to fit an M696 midpipe. Not sure what your options are on 1100EVO. Stock exhaust systems dont generally tend to have removable baffles (unless you core 'em that is). There are other less costly options than Termis........
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If I understand correctly, I have to let the re-flasher (e.g, Mota-Lab) know what my configuration is and they will hook me up with the best map for it?
Yes.
well you can get a generic map which can cover slip ons and air filter
True
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or a custom map depending on your application, you can get custom maps made for you get a dyno sheet with the air/fuel, and send it with the ecu and if they can do a custom map to fix the a/f and they can make it run mint if its done right
If its done right, sure. You have to bear in mind that a custom map produced in this manner is the map tuner's (mota-lab, rexxer) best
estimation of what variation in fuelling will be required to get you from where you are to where you ideally need to go.