In terms of the midi foot switching, if you end up using the setlist/song feature, you can set up dedicated CC messages to select the specific song parts. This way you can use the same footswitches to select song parts 1-5 in every song.
In terms of the expression pedal, it also depends on how you are setting up everything in GP. If the plugin you want to control is in the local/standard rackspaces, then the easiest thing is to just set up the expression pedal widget in each rackspace. That way you can change what it controls from rackspace to rackspace.
Otherwise, there are always options/workarounds to get it working as you want.
I assume you’re on Mac? For MidGuitar2 you also have the option of running it outside of GP as a standalone app. It will create a Midi Port in GP so you can then route it to synth plugins within GP. This can have some advantages, such as offloading the processing work of MidiGuitar2 to other processors on your Mac - particularly helpful if you are pushing the limits of the machine with the plugins/setup you want to run.