proud new owner of an FJR :)

[RossKean]

That's normal. Mine does the same thing. I fill up with the bike on the side stand and the fuel pump nozzle just inside the big hole.

I usually try to squeeze in a bit more so the first bar lasts a bit longer... Just don't fill to the brim and then park your bike in a warm spot. It will mark its territory when the gas expands out the overflow hose due to heat (or flood the charcoal canister if you have a California model).

As far as removing the Power Commander, just take it out and put the connectors back to stock. It has no effect on the ECU programming.

Easy to do! Doesn't directly affect ECU programming but works by re-interpreting the ECU fuel injector control to richen the mix at low throttle openings (if programmed to smooth throttle response).
If you unplug the Power Commander to see if you can live with the more abrupt throttle response, remember to re-connect the O2 sensor - it is generally unplugged (but not removed) when a PC III is installed. (I think a wide-band O2 sensor is used for later model Power Commanders.)