So, if you remove those files you're considering removing, will you have completely ship-of-thesiused everything in 2xx04's repo from your repo?
Either way, just my $0.02, maybe it makes sense to just start a whole new repo. If you do need something from 2xx04's repo (like his fork of Bootstrap, maybe?), I'd say copy it into your repo and make sure the README.md links to 2xx04's repo and describes specifically what you copied and what's 2xx04's.