Would it be possible for me to basically remove everything that is selectable in nLite, then when selecting what files I want to keep, just keep the ones that are absolutely necessary for my install, programs, etc.?

Problem is that those programs usually need some of the reg entries of the needed component so your best bet is:

- remove all

- learn which components are needed and start keeping them with every new reinstall (save your preset)

I'm keeping only 5-6 components and all runs great, but for example you may be using analog Modem then you gotta keep 4-5 more components and so on...