I have uploaded my own screensaver to my Nook Simple Touch, but when I connect it to my computer via USB, the screensaver goes to one of the stock ones. Is there anyway to make it so that when in USB mode, my Nook displays my custom screensaver instead of stock?
Whenever you connect your Nook in USB mode your USB storage from Nook gets unmounted and mounts in your computer. After its unmounted the OS can no longer find your screensaver. That's why Android doesn't want you to keep widgets in USB storage. Similarly apps moved to USB storage no longer works while connected to your computer.
If you move the screensaver to internal partition then it will work even when mounted to computer. For this your Nook must be rooted.