Had a chance to do some testing tonight and have hit a roadbump, when the VG-99 and FC-300 are in SysEx mode, and you set to output #CC when you hit buttons on the FC-300, they are all in momentary and not latching. Changing performance/slot worked a treat, as did the Exp pedals, but the problem is the FX slots are only active as long as you hold the button down on the FC. Not cool.
I may have thought of a work around tho, I'm hunting for a MIDI Solutions Event Processor, which can convert #CC to NRPN (to control the advanced functions of the KPA) but also ignore #CC. If I set it to ignore the "off" part of the #CC, I should be able to activate a FX slot in the KPA and not have it turn off. Obviously then to turn it off, I would have to reset the rig, hopefully by just pressing the patch (#PC) button on the FC-300, but worst case is switching to a different slot and back again. Not ideal but I really want to use just one foot controller.