You're making this way too hard.
There is no such thing as an upgraded exhaust, just LOUDER exhausts. Put a stock muffler on it, put the stock air cleaner on it and just ride it. The bike makes 101 HP stock. If you're buying this bike for all-out horsepower, you're buying the wrong bike.
All the aftermarket air cleaners will be a problem when they get wet (you said you want to tour on it). There is nothing wrong with the fuel injection if you just ride it and fix any broken sensors. If you don't screw with the exhaust or the intake, you don't need to screw with the fuel mapping and sure as hell don't need a race ECM.
AFAIK, the only thing the race ECM does is eliminate the rev limiter. You gonna' rev the piss out of a pushrod twin?
Just ride it.