IN RE MIDI CONTROLLERS:

I use a Disaster Area DMC-3XL. But there are tons. It is 4.8″ x 2.6″ x 1.4″

You could control 3 H9s with this if you wanted. but in banks for each pedal.. or you can call PC messages on all of them simultaneously for coordinated switches. 

IN RE REWIRING:

This would be trivial, I think. The switches are panel mounted.. so you could clip them easily. Then you would have to wire onto the inside of the jack… on the right side of the attached pic,,,but it is outside of the audio signal chain.. so pretty low-risk, IMO.

It would take an hour and 2cents worth of wire.. and would be a killer mod.  You should do it!