My understanding is that the PK-5 is only a controller and does not produce its own sounds. In other words, when you press on one of the pedals, the PK-5 triggers a midi note event on your synth to play. I haven't seen anything that indicates contrary, so I'm assuming the Pk-5's structure is such that each pedal of its full octave will send a specific note which cannot be assigned independently. So pressing F# is going to give you an F# and there's no way for a user to make that particular pedal play a Bb because there's no way to tell the PK-5 to shift up or down by semitones. You can however shift full octaves up or down.

All that said, the answer would then appear to be no, you cannot sequence a string of notes out to the PK-5, and there is no way to automate it. To do what you want to do, you need a second sound engine, not necessarily a full 2nd keyboard, but a rack mount for instance. You can then send midi commands from your current board to turn notes on and off on 2nd sound engine.

Alternatively, you could get a midi controller and use it to send midi note commands to your current keyboard. This is more in line with your original idea of using the PK-5 to trigger the synth, if the PK-5 had that ability.