EFI mapping is based on intake, combustion, and exhaust of a fuel/air mix. change any part of the equation and you have to re-balance things.
Removing the cat/con reduces exhaust back pressure (increasing air flow - at least in the exhaust pulse). On the FJR the cat/con has more of an influence over the exhaust side of the "air pump" (engine) than the muffler does. You can swap a muffler on an FJR and it will have little affect on the engine as long as the cat/con remains in place (where the bulk of the back pressure is created).
After removing the cat/con an unchanged EFI is still sending the same amount of fuel into a mix with increased amounts of air... this is known as a "lean" mix. Most bikes these days already come at the ragged edge of lean to pass emissions tests. Making the bike run even leaner would concern me and send me to a Power Commander dealership followed by scheduling a trip to a trusted dyno shop to get a proper map for your new setup. Since dyno time at a reliable shop is costly, consider what you might want to change on the intake side of the pump while you're doing things. Some people don't like foam air filters, but if that's okay with you, doing the swap before heading to the dyno shop would be the time to do it. It would avoid going back to the shop multiple times for dyno runs each time you made a change to intake/exhaust/etc.
But that's just me.