If only you had done this when first asked - would have saved you and us all a lot of time. Please remember this second account trick for any future weird problems. It really is the thing to do first for really weird stuff like this.
The thing about all those plist files - there are a lot of them and control all kinds of settings. Some apps may not even run if things like license numbers and such are squirreled away in them.
But, now that you have a pretty good case for a corrupt plist file, I would start by booting up in single user mode by using Command+s. Do you have everything on the one internal drive (system and all your /Users files)? If so, then just follow the instructions that are on your screen to do a "fsck" and then mount the boot volume so it's writable.
Then, do the following (all these are Terminal commands and substitute your real user name that is bad for "yourusername"):
cd /Users/yourusername/Library
mv Preferences Preferences.bogus
sync ; sync ; sync
reboot
Don't forget, that you're the "root" user and you can do some real harm if you give a wrong command so be very careful and ask first if you're not clear about anything.
The system will reboot, and you can try to login in. The OS will recreate the Preferences folder and populate with defaults but things will behave differently than you're used to - some in minor ways and some in major ways. If everything works OK, then you can try copying the Preferences over from the bogus folder to the real Preferences folder in some ordered fashion being very careful of putting them in exactly the right place. If you don't understand how to do this, then ask and can give some hints. It's gonna be time consuming as you need to logout and back in and try and find the plist file that is the culprit every time you copy a plist file or group of them.
If you're happy with the way things work with the new set of default preferences you have, then you might not want to even bother finding out what the problem was, but that has to be your decision.
Now the bad news, if it wasn't something in one of the files in your ~/Library/Preferences folder that was causing the problem, then you need to undo moving the Preferences folder (reboot back to single user and do the reverse) and start looking for other places to do something similar - places like ~/Library/Containers or ~/Library/Application Support and on and on. That gets to be a giant pain in the rear. So lets hope you get lucky...
Ask questions if something isn't clear and be careful in single user mode. You really can do some bad things if you're not careful.
Good luck...
ps -- if anyone else sees any problem with this method please speak up. I've never had to do this but seems that it should work. In fact I think rywag should try the method out first on the second user account first before trying it out on your real problem account. The idea being that if there are any side affects that are big problems you will find out about them in the second account rather than the real account. Make sure you have a full backup in case you have to restore anything and double check it's integrity before doing any of this.