Setup:

• Windows 10
• i5-4670k @ 4.0GHz
• GIGABYTE|GA-Z87X-D3H mobo
• (2) GTX 980 SC ACX 2.0
• 4x4GB GSKILL @ 2133MHz RAM
• Acer XB270HU Predator Monitor - 1440p
• Corsair AX850 PSU

My setup was fine until I bumped up the power limit to 110% for benchmarking and enabled Kboost with slightly higher clocks than normal - 1400 MHz core and 7100 MHz memory.
 
I don't seem to be getting anywhere near 100% usage on both cards in any game anymore... Valley Mark and Heaven mark my second GPU seem to hit about 80-90% but they fluctuate a lot. Is this a power issue? Voltage doesn't seem to fluctuate, though.

Both of my cards were reset to default clocks and voltages. OC'd my CPU back to 4.2GHz to see if it was a bottleneck but no change there...

With stock clocks I'm not getting 100% use on either card now in any game but BF4, but only when in menus (used to get mid-high 90s during gameplay).  GPU usage in BF4 jump between 55-80% while playnig/ 99% while in menus; ~60% usage from both cards in ROTR.
Temps stay below 60C.
 
Can anyone help?  Suggestions?

Try testing each card one at a time to see if you can get either card to go to 100% usage under load. If not already done, remove the driver with DDU and do a custom install with just the main graphics driver and test both cards by themselves and configured in SLI. 

You also may want to check the PSU with a multimeter or at least check the +12v reading in BIOS to see if you are getting consistent voltages.

Place your better card in slot 1.
 
Turn OFF Kboost for gaming
 
Does your MB & CPU combo support PCIe 3.0 ?

OK, so I tried Heaven again after switching GPU slots and I got tons of artifacts.  So I ran DDU and uninstalled Afterburner and its profiles.  Reinstalled a clean driver and the artifacts went away.  Got some good usage out of both cards with decent FPS in Heaven this time around.
 
Started to play ROTR again and tried at Medium settings and raised the settings until they were on High.  The Both GPUs usage never went above 75%.  Open areas were lower usage than close quarters.  MY FPS stayed about the same in both Medium and High settings (weird).
 
I played some Star Wars Battlefront and the usage, again, didn't really go over 75% on either GPU.  I got normal FPS and it was buttery smooth play.
 
BF4 multiplayer is still having the same issues.  I'm getting decent FPS for a 144Hz @ 1440p monitor (80-110FPS) while playing, but once the round ends and the cut-scene thing plays behind the scoreboard it goes back up to 99%.  I get 99% usage in menus too, but always drops once I go back into the game.  I'm going to run a few more tests, but this isn't making any sense because I wasn't getting this bad of performance before.  The first GPU was always running at 99-100% while the bottom floated between 65-99% depending on the game.
 
I checked Voltages from the BIOS and they look fine so I think I can maybe rule that one out at least.  
 
The cards run fine in a bench-marking environment, but not in a game environment.

Any update?
 
Have we tried single card?
 
Has the PSU been tested?

have you ran SLI before?
 
What is max refresh on your monitor?

Unfortunately...yes. There's a 900 series bios mod by request thread @ overclock.net/f/69/nvidia. Just post what you want along with the stock bios and you'll have the mod bios in less than 24 hours.

It apparently does.  Like I said before, I used to get 99% usage on my first GPU and ~80% on my second with higher FPS before all this weird SLI stiff started happening.

I want to ensure you understand that the idea of SLI is to not have the GPU usage at 100%. It's supposed to bring that usage down while still maintaining great temperatures and having a much higher FPS rate, compared to running only 1 GPU. I'm not questioning your knowledge of SLI, but just making sure that we're on the same page when it comes to that. your first post sounds like you're trying to make your GPUs' usage run at 100%. You don't really want that.
Also, it doesn't look like your game, ROTR, has enough processing where it's going to put the 980s on their knees. the 980s are amazing cards. I have the same, and have zero issues. Your 980s will keep you going for a very long time. don't lose faith in them.