So, I think I going to attempt both approaches. I had dragged my System HDF over before I had even asked the question just in case you weren't around to answer. By the time I went to bed, my System HDF had moved over. Using AExplorer, I was able to easily verify that the HDF I'd copied to PC was the exact same file size as the HDF on the Amiga.
So, I exhaled a bit. My System folder is only 9MB. The transfer, at the end of the day, took about an hour or so. Not too shabby, really. So then tonight I'll probably drag the "Fun" partition over, which is 41MB. That will take, presumably, 5-6 hours.
After that is done, I think I'll do it your way - moving folders over in batches, so I can easily manipulate the internals. At least this way I'll have a snapshot of my current system and configuration. So if anything horrible ever went wrong, I'd have a "Time Machine" I can go back to in a pinch. Space is cheap for me on the PC side.
Once I've moved all of these files over this week, I'll breath a little sigh of relief. I may even move those files over to DropBox, as yet another fail safe (I have a pro account, which is a massive 1TB). We also use Google Drive at work (and I think we're upgrading the size on that soon, too), but I try hard not to mix personal with work. In other words, I've got too many storage options.
After this is all sorted this week, my next task I want to wrap my head around is how to restore one of these HDFs (or folders within) to a new drive for the 2000. I know how to install WB 1.3 to HD (I think) and how to partition drives using Fast Prep, but I'm not sure how to start from scratch. It's something I need to educate myself about. First things first, though. Backups!