L&LD
Part of the Furniture
@PuckHead, are we talking about the RT-AC88U router all this time? 
Try unplugging everything from it (Ethernet cables, USB cables/drives, WAN cable, Power cable, etc.) and leave it unplugged (but with the power switch 'on') for a couple of minutes.
Plug everything in again and see if you can get full 1GbE Port connection rates.
If that works, you may also want to not use the 5 to 8 Ports on the router either (they are known to be on a flakey switch).

Try unplugging everything from it (Ethernet cables, USB cables/drives, WAN cable, Power cable, etc.) and leave it unplugged (but with the power switch 'on') for a couple of minutes.
Plug everything in again and see if you can get full 1GbE Port connection rates.
If that works, you may also want to not use the 5 to 8 Ports on the router either (they are known to be on a flakey switch).