For problem 1, are you sending a PC first and then sending the CC message to switch to perform mode?

For your looper transport issues, it sounds like your MIDI CCs are not setup correctly. The CC message needs to send a high value when the footswitch is pressed, followed by a low value when the footswitch is released. Please confirm your MC4 is configured to do this.

See #3 for how to use H90 Control to assign the external controller mappings: https://cdn.eventideaudio.com/manuals/h90/1.12.5/content/h90-control/edit.html#control-assignments