Can TrueTime and TrueCoverage instrument specific files?
Yes. You can use NMOnly switch for NMCL when you instrument your application from the command line ( for more details please refer to the help file).
After you do a regular build without our tools involved, just 'touch' the file that you want to instrument, for instance, add white spaces into that file, and then do a 'build with TrueTime' inside VC IDE. By doing so, TrueTime/TrueCoverage will only instrument the file you just touched.