A quick follow up on this. I've reinstalled all the apps and somehow gained a staggering 100 gigs in drive space with the clean install. I tried a restart with the option key pressed to see if the recovery drive would show up and it's still not appearing, although disk utility shows a space of 1.21 gigs listed as other, which may well be the recovery drive. The only real pain is that for some weird reason Mail is now refusing to read the data that I copied over from Time Machine. The accounts were all set up automatically when I signed into to iCloud, but none of my archived messages are showing up now. It's really perplexing and the first time I've had an issue like this in over 15 years with Mail.