Trouble uninstalling and reinstalling

I've been running Civ 4 on my Windows 8.1 computer for about three years with zero issues. (Have the Amazon download version). A few days ago I downloaded a screwed up mod that overwrote several game files to the point where the game no longer ran properly (e.g. I'll load it and a bunch of units will disappear or the only thing i can build from the city menu is 15 different instances of worker). I've tried several times to uninstall and reinstall the game but I keep having the same problem.

When I load the game after reinstalling it still has all my graphics settings and such which are not the default, so I wonder if there's some civ 4 files that are not getting deleted and lead to the problem recurring. When I uninstall, I uninstall via the add/remove programs in control panel, then I completely delete the my games/beyond the sword and my games/colonization folders as well as the 2k games/firaxis folder. Is there anything else I have to do? What am I missing? As I mentioned I've been running successfully on this particular computer and OS for years so it's not a "running on Windows 8" issue or anything like that.

(By the way, do not by any means try installing the Ultimate Edition Road to War mod currently up (as of 2/4/16)- that's what started all the problems in the first place...

There's also cache and profile data. If it's the same location as in Windows 7: users -> user name -> appdata -> local -> my games