And I tried to download some mods with the NMM, but realized that was still in C.

So I copied and pasted NMM folder to D, my new HDD, and deleted the copy in C. Is that all I have to do?

I then ran it, and no mods are listen in the mod menu. Im not sure if theyre still in my game or not, or even what mods there were in the NMM, as most of my mods I just put into the data folder.