If your going to take the time to open up the motor, you should just rebuild it with forged internals. If you need to overbore it, that would mean you would need new pistons anyhow, so now your talking about just replacing rods and bearings and having a crank polished. It would only cost you about $800 more to get performance parts, rather than use stockers. This would leave you with a nice platform to build off of in the future.
As far as your questions about the motor cycle tuner and FMU. You need to check the flow rating of the FMU, it might be able to make pressure but not supply the volume of a car. Also with the engine management, does that thing have perameters for a 4 cylinder engine? It needs to be able to control 4 injectors and 4 ignition sequences simulaneously. Also, what signal does it use from the bike to make changes? Is it a mechanical crank/cam triiger? Is it magnetic? Is it a hall effect type sensor? The controller needs input from the motor to make changes and see results, need to make sure its the same type of signals.
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