Two R7000 connected via a CAT6 cable but showing AMBER lights on 4 LAN ports.

Assuming that there's still interest...

> I have a FIOS gateway router (basement) as my main [...]

   Has it a maker and model number?

> [...] and two Netgear R7000 (family room & upstairs hall), [...]

   Firmware version(s)?  Configured as routers, or as wireless access
points, or what?

> [...] all connected via CAT6 cable. [...]

   If a device has different types of Ethernet ports, then "connected to
device" is not enough detail.  What, exactly, is connected to what,
exactly?

> [...] the upstairs hall R7000 router where all 4 LAN port lights are
> showing AMBER [...]

   And what's connected to them?

> What the heck is going on?!!!

   Sounds like bad cable(s), but many things are possible.

   For a quick cable test, connect each end to a LAN Ethernet port on an
R7000, and observe the relevant port-status LED indicators.  For a good
cable, both port-status LEDs should indicate a maximum-speed connection.
(And they should agree.)  On an R7000, that would mean white port-status
LEDs.

   When you have identified a good cable, try using it to connect a
couple of R7000 units together (however you want to do that).  Start
with a less complex configuration, and build slowly.

   Visit http://netgear.com/support , put in your model number, and look
for Documentation.  Get the User Manual.  Read.  Look for the LED
descriptions and "Troubleshoot".

> [...] The Amber light means [...]

   What it says in the User Manual.

> [...] Do you have devices that are transmitting at 100Mbs (say older
> computers or laptops) or all they all transmitting at a gig (1000 Mbs).
> [...]

   Presumably, when connecting two R7000 routers, all the ports involved
are gigabit-capable.  Whether the cables are is a different question.