If your old C drive goes back a few years they might be there from when V4 needed to be in the main runtime which is not required now,  

Actually that statement is incorrect.  V4 base and all her morph packages should be in the same runtime regardless whether they reside in the main runtime or external.  The main runtime concept arose because Microsoft Vista and Win 7 did not exist at the time to complicate security issues.  Also, it was convenient to instruct new users to place files into an established location rather than detailing how to create external runtimes.