Doesn't the GR manual describe how to do all this?
From memory, the issue is that you are recording onto an audio track with GR on it, and twiddling the pedal sends MIDI info, which obviously can't be recorded onto an audio track (because it's MIDI). And the effects of the pedal won't be printed into the audio, because you ar printing the guitar sound
before it's processed with GR, so it's just the dry sound.
If you want to print GR, you can use it on an input channel, rather than on the destination recording track. This uses GR pre-tape, and thus the audio from GR is recorded, not the dry guitar signal (you could always record that as well, to give you options).
Lastly, you could probably also record-enable a MIDI track and record the MIDI data the pedal sends during the performance, and play it back to GR to replicate your pedal moves...
But I'm sure the manual talks about all this...