I agree that starting clean, working through vimtutor and giving it a solid week (but going ahead and installing plugins to make it work how you need to actually do something) is the way to get it to stick.

Once you are the point of using Pathogen, you should also consider using Vundle for similar benefits but easier module management (update, uninstall)... with Pathogen you end up rolling your own stuff with git submodules or something and that's fine but it's already done in Vundle.