I understand your position better now. I didn't realise (or forgot) that bass is your main instrument, so can see how you'd be torn over the investment in files.
The DIY feeler gauge nut files do work, but making them (properly) is time consuming. However, you only have to do it once.
You can probably get where you need to be by working with both the nozzle cleaners and modified feeler gauges. (rough in with feeler gauge, clean up with nozzle reamer)
As for top or bottom of nut, really either is fine. It's more personal preference as well as what the end goal is. If you have a nut that's too high but already has perfectly cut string slots, it may make more sense to take off material from the bottom, whether radiused or flat.