I was so angry that I deleted a lot of the new character files directly from the Characters directory.
This pretty much kills a neighborhood. Deleting files out of the Characters folder does not fully delete sims, and their garbage will continue to clog up the neighborhood file, or possibly even corrupt it completely. Unless you planned to spend a lot of time fixing the mess in SimPE, you should not have deleted any of those character files.
You also did a bad thing when you kept one member of a family while deleting others. This should never be done. Or, not unless you know exactly how to fix the mess in SimPE.
After that, of course, that neighborhood won't load any more *rolls eyes*. I don't know why, I don't think it could be regenerating strays, since I have nostrayregen installed. I'm restoring from backup right now. How can I get rid of these unwanted families and strays without destroying my neighborhood again?
Use my Empty Templates (found in Peasantry). You will never again get any unwanted sims in any of your neighborhoods, no matter how many subhoods you attach. You will still need all of Pescado's norespawn hacks, which are: notownieregen, nossrespawn, nostrayrespawn, nodormierespawn, and antiredundancy. Check for EP compatibility, of course.