I just realized I haven't updated this project in a _very_ long time!
I've been actually busy troubleshooting the shields, and making my way through designing the blocks for programming.
The analog multiplexing shield run OK, and allows for reading up to 64 analog inputs through Arduino A0 (can be changed to A1).
The digital matrix took quite a long time debugging. I mounted two individual MCP23X08 on the shield in a matrix configuration, and used the inbuilt interrupt pin to signal the Arduino to check the state of the pins. Most of the debugging was due to the elusive "digitalPinToInterrupt(pin)", as in:
attachInterrupt(digitalPinToInterrupt(pin), ISR, mode);
For some reason this function call is needed when using an Uno (didn't use to be), and it took quite a long time for me to find that out. There is very little detail on that function call, and it seems older code that does not include it doesn't work anymore.
On the topic of the digital matrix shield and the use of two MCP23X08 - I think I'll change that up for a single MCP23X17, and also get rid of all the unnecessary diodes and resistors. I believe that the I/O function of the chip itself should be good enough for what I'll be using it, especially with the built in pullup resistors.
I settled on Ardublockly as my block programming UI. It's both better documented and has got a better support network (through Google's Blockly). It also looks nice, and it's looks can be further tuned through CSS. In the following image are the blocks designed for this project up till now. Far from completion, It's a start, and I'll be designing the blocks for the next few weeks, to get the quick drag-n-drop MIDI capabilities I want.