That's a lot of stuff
I can't say for sure since I don't know how quick is quick.
So if I may dissect your project, I'd do this:
inputs: some dozens of buttons (although this can be better done with matrix connections, in which case you just need 14 input lines, 7 rows and 7 columns, so 2x 4021N)
inputs: analog knobs with ADC. I don't know too much about ADCs, I suppose they're on SPI bus so no problem.
outputs: LEDs I would separate the LEDs from SPI CS lines just because they're different and coupling them would be more difficult to debug.
You can use two separate latch lines, first one goes to 9 shift registers controlling LEDs (make sure your chip can connect 9 in series, I doubt it is a problem though), then a second latch line goes to the last shift register. This way you just shift away whatever you need and toggle the right latch to update LEDs or SPI CS lines, two things are separate and yet still you save I/O pins.
What clock and control data do you need?
My overall feeling of the entire