I suggest lubing your throttle cables, and be sure you don't have any corrosion in them, or have them too-tight/not-enough slack. You can try doing it with everything hooked-up, but I suggest disconnecting the cables, checking them individually for drag, resistance, and then re-connecting them and make sure you have a few mm of slack. Having them too-tight will give you an erratic idle, and drive you crazy trying to fix it, by 'adjusting' the air needle, cleaning the carbs, adjusting the floats in the bowls, synching, and everything-else, when it's just a matter of too-much tension on the cables. The helix, the spiral jacket in-which the cable runs, can develop corrosion over time, and the corrosion can hang-up the cable(s) so they drag in the outside housing.
I'm not sure if the FCR carbs use the VBoost or not, I think that if you follow the Dynojet Stage 7 directions, and eliminate the butterflies, there is only one type of balancing tool you can use. I think no-butterflies makes the liquid Motion Pro synch tool not work correctly, because you cannot isolate one carb from-another. Dannymax or Sean Morley can probably inform you in more-detail.