Having the saved games on a separate drive to the core files is not an issue, that's how I run it.
Just as a point of sanity, what's the failure mode being seen? Once you have 'installed' the mod, can you see the units in the mission editor? Can the NTTR mission be opened (I see it says the mod is required but that will be shown all the time, even if its installed).
Do you have two installs of DCS? Maybe an Open beta and a Stable and the mod is installed in the wrong one?