I have SCMDraft installed on my Flash drive.. and SC installed there as well... it was working okay for every computer i've used except the one I am on now, for some reason it wants to use the StarDat.Mpq in the Starcraft folder instead of the one in its folder...

The problem is now that the flash drives letter changed from (E:) to (F:) and now when I attempt to open SCMDraft it says Fatal Error: Failed loading primary MPQ (E:\Starcraft\stardat.mpq)

Anyone know how to reset it so I can reassign the location?

Go into your Draft profile setting and change the stardat.mpq directory.