74HC595 multiplexing + bit angle modulation and UNO questions

Just typed a bunch of information, but connection timed out... And I gotta leave shortly, so this will be vague

I'm making a modular program to attach different multiple LED output devices and input controllers. The main aim of this is to keep all output devices in sync with each other and each output device will have some controls on separate input devices AND keep latency very low, all on one UNO preferably. I wanna change a few variables at the top to tell it which devices are connected in what order. I've never built anything or made a program in arduino, but I have the theory down (electrical physics and programming background) pretty good I think.

  1. daisy chain devices by chaining shift registers? Should I use 1 'master' shift register for global timing or keep each device independently functional?

  2. multiplex into the least shift registers or multiplex as little as possible

2.5) minimize or maximize PIN usage?

  1. ~32KB memory and 2KB variable memory translates to approx how many lines of code and ~1000 int variables, right?

  2. Utilizing persistence of vision; what's the best way to utilize this without loosing substantial brightness or the ability to at least dim in a few levels with no major latency (via bit angle modulation, preferably)

I might have some power supply questions depending on the answers, but I don't have time for that right now. Thanks in advance, I hope to repay the community down the road, but this is all new to me