We should be back to normal operations. The only major hitch in the upgrade proceedings was that midway through running the final 4.1 upgrade script, mt-wizard.cgi, my web hosting service (who had asked me to run this upgrade in the first place) shut down my access to the script for drawing down too many server resources. Having spent an entire weekend afternoon running backups and troubleshooting, I was not happy. Fortunately they responded quickly to an email about the shutdown and I was able to conclude running the upgrade this morning.
I'm still not sure what caused the original server load problem - I'm off to compare my custom blog index template with one of the default templates, to see if I can find something to fix there. Right now I suspect the issue is something to do with the image upload process, since that was where MovableType was slowing to a crawl before I updated, and I need to figure out if the update fixed that.
Postscript: And comments are broken. So that's the first thing to fix.