What happened to the NTTR scenery and Nellis AFB V2? I can only find v1 FSX.

I didn't think there was a v2.

The only changes made to the KLSV scenery was the update to make it compatible with P3Dv4 for the Matrix product, as far as I'm aware. That update was withdrawn along with Matrix a few years ago. OP has just transitioned to FSX:SE, I believe, and the FS9 KLSV should work in that sim.

In case P3D is what OP is now interested in, there was a thread that covered getting it to work in P3Dv4/5 after the Matrix version was withdrawn. It's here.