sure no problem Larry.
If you don't have need for cue files, I just wouldn't import them. (or maybe even think of physically removing them if they serve no purpose.) If you want to prevent JRiver from importing certain file type just go to your import options and on the paths you are "watching" hit the edit button ... under each media type you can click on the file extensions you want or don't want. The only reason you might need cue sheets is if you have one large file for an entire album (I'm not a big fan of this personally) - then of course you need the cue file to break out the tracks. Maybe you were using EAC back in the day and the cue sheets remained? Just guessing though
You can use audio analysis on import (I don't, i have a smartlist that indicates what hasn't been analyzed and I run it manually. It makes my import that much faster as audio analysis takes some time. I was guessing that the program was hanging because it was trying to analyze cue files that no longer had files associated with them. If you aren't importing them anymore ... you can turn this option back on.
As for that big ISO file from John Doe you might or might not have loaded, I have no idea how to get your OS back to its original state frankly. I'd hate to steer you wrong about how to go about it, short of a clean Windows install. Maybe if/when you change to Win10 this would solve itself, but then again it might be ported over too. Sorry I don't really know.