I think your project might be a bit ambitious for a single Arduino. Your control surface objects represent a large number of I/O pins, so at the very least begin by looking at the Arduino Mega series. I then see a lot of tying together different modules and worrying about pin conflicts and such. You might be able to prototype each of the individual components of your control surface but putting the whole thing together into a cohesive whole will be tough.
You should probably begin with a big system block diagram of all the components you want and sketch how they will interconnect with each other, what protocols they will use (SPI? I2C?) how many I/O pins each one takes up, what kind of hardware resources are required for each (interrupts, timers, etc.)
As for converting from one platform to another, of course anything is possible if you replace the chip and replace the "programming", as you say. But it could be a fair amount of re-programming, as each microcontroller platform comes with its own set of peripherals and resource limitations.
Maybe start small and add things one at a time, then grow to a bigger system if necessary.
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The Arduino Drum Machine: MIDI development system with 14-track MIDI drum machine sequencer / groove-box software