Please don't apologize for a late reply. I feel very appreciative that you put the time and effort in at all. A couple of things:
1. Do you consider DropBox and Evernote in the same class of file sharing as Peer-to-Peer, when I'm only sharing files to family & friends through invitation?
2. Just to be clear on SPAM, sometimes things accidentally get looked at (opened) that are spam. Other than sending a notification back to the spammer (and thus verifying your address), can just opening it cause infection if no links are clicked?
3. My control panel shows 2 versions of Java. The one I just updated is "JavaFX 2.1.1" and the other is "Java(TM) 7 Update 5" but with a date of June 1st. Should I delete either of these?
4-7. So if I upgrade to Malwarebytes, that will give me real-time malware (but not virus) protection, Microsoft Security Essentials will give me real-time virus and malware protection, and SpyBot can be run regularly as an extra layer of virus and malware protection. Do I need firewall protection, or would Microsoft Security Essentials provide this?
8. I'll take your advice on a system upgrade, and steering clear of registry cleaners. But since I'd already run RegZooka, which deleted hundreds of items, is there a tool I can run to make sure my registries are currently in order?
9. Does SpyBot include connected external drives or devices when it runs? From this point, now that this computer's clean, and once I upgrade my virus protection, will it be safe to simply connect externals and scan them (and will zipped or archived files get scanned)?
10. Should I now uninstall HouseCall, aswMBR, ERUNDT, OTL, and dds, or could they be useful to me in ongoing system care?
11. Is it ever recommended, or not recommended for a relative novice like me to scan for viruses/malware in safe mode?
I'll spend some time reading the pages you've linked to (this one's broken: http://forums.whatthetech.com/index.php?showtopic=57817). Thank you so much for your support. It's nice having a functioning computer again.