The extra details provide a better picture of what you are trying to do. Looking it over, appears doable albeit with some tweaks esp with the installation being necessary. This isn't the easiest, most straight forward method(s) however.
larason2 wrote:The Mega encoder you bought is designed to work with a matrix you make yourself using diodes. It’s not too hard to do this wiring, and that’s probably the easiest to wire up your manuals. You will need probably about 200 diodes, and you can use the cheapest signaling diodes you can find..
If you need a source for 8 X 8 (or 8 X 4) matrix boards, Gino has these
https://www.shop.gino-midi.nl/product/decoder-met-matrix-bouwpakket-2/?lang=enI have bought these raw, unpopulated boards from Gino as a special order item. Some re-wiring is necessary to the output IDE header, A raw PCB makes this easier. Also, after placing such a special order item(s), you may need to wait for Gino to place a new order for these boards, as he would add your order to his order.
An alternate options are to use the Midi Boutique board made for this setup as larason2 suggested.
Have you tried disconnecting everything from the Arduino Mega encoder board and wire just the pedal matrix board to see how that works independent of everything else. A basic trouble shooting technique. BTW, what are you using for the pedal board 8 X 4 matrix board?
From the encoder details,
https://www.midikits.net/midi_3_8x8_8x4_8x5_3_exp/switches_8x4_PB_Bass_ct.gifAgain, if wired properly with a correct pedal board matrix, this should work. The Arduino Mega is certainly capable. From everything you've said so far, I'd focus on the pedal board matrix and these connections. Disconnecting everything else eliminates everything else from being involved with the problem.
Rgds,
Ed