I want to eventually go water-methanol injection. I hear our ECU's are very picky. I don't want to install water-methanol injection if I can't reap the actual benefits of it.
You don't need a custom tune to take advantage of water/meth injection. Common practice would be to run an aggressive tune. Example: get the Stage 1 100 octane file from APR. Run 91 or 93 octane fuel in your tank and use water/methanol to add to your fueling. This will allow you to run a race file daily. I have been running a race file on my K04 MKV this way for over 2 years. The added benefit of water meth is that it can cool your intake temps in a way that even the largest intercooler cannot. I live in a very hot climate, over 100 degrees in the heat of summer. With water meth I get very little power degradation in the heat.
Note: Methanol has an octane rating of 116 octane.
In general you spray far away from intake manifold for cooling, as close as possible to intake manifold for fueling. For instance I spray using 2 nozzles. 1 nozzle just after the intercooler (cooling) and one nozzle in a throttle body plate bolted to the intake manifold (fueling). You spray close so the w/m mix gets into the cylinder as droplets (not evaporated) so it can be used as fuel.
Basically you get the 100 octane tune, then you dial in the water meth system to meet the fueling needs of the tune. There is more to all this but this is the abbreviated version of how to get the most out of water meth.