It is a little annoying, but backing up your data and settings and installing the Rom works. I always have to rerun my preferred remove scripts after a Rom reinstall. This is what I do.
I don't like to give out false information, but I think I read you can just extract the apk file from the Rom itself, I suppose that is with 7zip and the Rom file on your PC. I suggested (or supposed) 7zip because when I was researching how to theme applications 7zip was always mentioned in place of WinRAR to extract the . PNG files needed for theming. I am already a 7zip user as I run Tiny XP rev 09. And 10th and they come with it. I can tell you I prefer it over other archivers.
All typos I declare my new HTC IME fault because I'm trying to swipe words on it lol. But its still very cool keyboard when customized to match your bugless theme.