General :: Saving User Account Settings When Reinstalling?

When I reinstall my distro (MEPIS, for the last 2.5 years), making my new user account preserve all the old account's settings has always been a difficult and very messy process, especially if I have installed a new copy on another partition. (I'm doing that soon, so I have this copy as a backup until I have everything the way I want it on the new copy.) Most of my stuff gets saved, but not everything. The biggest problem is that, even if I select "preserve data in /home" in the MEPIS installer, my keyboard shortcuts become unusable (not completely erased) under odd circumstances. They're still listed in file /home/josh/kde/share/config/khotkeysrc, but they still can't be used, and I have to open hhotkeysrc and manually delete them and then reenter them in the menu editor (the K menu, by the way, gets completely overwritten).

I can't just overwrite the entire new user account with the old one; I've tried, and something goes wrong so that the new account can't be opened (probably because some important files are inaccessible--I can't tell which ones they become inaccessible).Anyway, is there a program that can preserve all the user account settings neatly for a new installation of the distro? I am supposing there is a program or at least a method, because I never hear others complaining about this problem. I probably don't know something I should know.