Did you configure each IA for general use by setting its Axe-FX function to NONE? Have you adjusted any values described in MFC manual sections 12.4.8 through 12.4.10?
12.4.10 covers program changes so you may want to start with this. Select the "pON" command, choose the desired PC# and pedal channel. This should select a preset when the IA is switched on, and do nothing when it's switched off.
Based on one Eventide manual (PitchFactor) a bypass CC# is user-configurable. Have you set or checked these settings on the pedals? Once you've done that, use MFC manual sections 12.4.8-12.4.9 to configure a 0/127 toggle for a pedal's bypass CC#. The 127 would be redundant if the "on" PC command engages the effect but shouldn't cause any problems.
Making IA11 select a preset on another pedal would involve either a custom MIDI message for a PC on that pedal's channel, or setting both to the same channel so the single PC from earlier recalls the same preset # on both. Set this pedal's bypass CC# to something different from the first if you don't want it to bypass when the IA is switched off.