Resetting Spotlight and giving it uninterrupted indexing time helped. Mac is still slightly choppy.. The firmware re-sets did not:
- System Preferences/Spotlight/Privacy: In the Prevent Spotlight.... window, I added my entire Macbook Air drive (13", mid-2013).
- Reboot. You should notice that Spotlight can't find anything, including applications
- System Preferences/Security & Privacy/Privacy/Advanced: I unchecked the "Log Out ...." box so that indexing is never interrupted. My screen was still set to lock after 1 minute
- Shut down all applications, plugged in the Mac
- System Preferences/Spotlight/Privacy: In the Prevent Spotlight.... window, I removed the prohibition from indexing my drive (13", mid-2013).
- Left the computer on over night.
The next day, everything worked fine, except Mail which kept crashing. I reboot somewhat solved the problem, but Mail is a bit choppy and still occasionally crashes. Best of luck to all.