Having problem with m.2, and gpu. Any help would be nice

I have an asus x99 deluxe motherboard and a 980 ti in the first pcie slot but for some reason it is running at 8x instead of 16x. Is it because I have the 3.1 usb header below it?

The other problem is in the bios my samsung xp941 m.2 is not showing up as a storage option is it because it isn't sata?

By default the M2 is turned off - you can turn it on in the BIOS.

How are you telling the speed on the 980ti? I have a 980 on an Asus board but don't know the transfer rate it's running at (thinking about it - probably windows app for it... I don't get to see that as I'm on Linux)

pcie gen 3 is usually at x8 anyway (thats gen2 x16 speeds) cards still dont realy even saturate gen 2 speeds antill you try crossfire or Sli