It seems to me I had similar concerns when I switched. In particular copy, cut and paste. I ended up using the CUA standard versions:
http://en.wikipedia.org/wiki/IBM_Common_User_Access#Descript.... Although looking back I think the awkwardness had more to do with muscle memory than anything else. I also was concerned when switching to vim. The purpose of using the motion keys h, j, k and l was defeated. I recall there being a dvorak layout for vim but I never switched to it. On the other hand, some of the other commands became much more convenient. Looking back I don't think it has been a big issue. What shortcuts in particular are you concerned with? You could always remap shortcuts using AutoHotKey or some other means. But I'd give muscle memory some time to build up first, unless there are some shortcuts you have found to be extremely inconvenient.