I can't figure out how to get the H9 to bypass as part of a preset from my Mastermind. 

Well, there are different ways to go about this. If you want to bypass a preset by sending out a MIDI CC, then you'd want to tie a particular MIDI CC message to the Bypass pedal function and send out a value of 127.  If you click on the Pedal button in the bottom menubar of H9 Control and go to MIDI Settings and then to Assign MIDI CC messages to pedal functions, you'll see the list of available pedal functions. There's also a pedal function for activating a preset or for toggling its state between active and bypass.  All of these functions should trigger when you send out a value of 127.

Other people save the presets either as Active or Bypassed on their H9s, and then they load them with MIDI program change messages.  If you load a preset with a MIDI program change message, it will load in the active or bypassed state that it was saved with.