Did you try completely removing all AMD drivers and Nvidia drivers with DDU Uninstaller before you swapped cards?

That's probably some driver problem... You will need maybe to install everything from beginning.
Smaller chance that something is not OK with that graphic card. 
AMD have own problems and customers complain there on stuttering even more. 
Special in CF and Dual Graphic cards, but I would choose rather R9-390X 8GB 512bit than GTX980 4GB 256bit.
reference R9-390X or XFX R9-390X 8GB Black Edition, 100MHz overclocked.
Simple because cards are very similar and R9-390X have much better bandwidth and memory video memory and I would sacrifice 5 fps for that. 
 
May I ask you why you cross on GTX980 from R9-290X, you should wait something powerful, difference between them is very small. 
What was problem with AMD R9-290X? With such cards water block is necessary, and for R9-290X and for R9-390X.
I even don't understand why people update cards with 7-8-10-12% difference and some quantity of video memory. 
 
You should check Windows Update for all necessary updates, and don't forget DX web update.  
It's fact that NVIDIA GeForce graphic cards work better with Intel i5 processor than AMD FX8xxx.
Many people notice similar behavior and combination AMD Processor + GeForce graphic card is the rarest combination. People usually choose AMD FX+ Radeon or Intel + GeForce/Radeon. Definitely you can try to OC processor little and improve speed per core, follow CPU temps maybe that help you little and try some of first drivers for GTX980. If situation with stuttering continue and with several drivers you could stay in line for step-up on GTX980Ti. Or you can sell GTX980 and upgrade on R9-390X 8GB, more memory will mean lot in next period and they work better with AMD FX. 
 
 
 

I assumed temperature problems, Hawaii is for water, now XFX R9-390X 8GB Black Edition, Double Dissipation cost 440e in Europe.
And I think it's best option after GTX980Ti, better even than Fury X. Second card for CF when price drop on 350-400 and nice configuration.
It's faster little than R9-290X.
 
I understand that changing CPU is not option but try with 350.12 or 347.88 or 347.52...
Some older drivers. Depend on game you can try with Adaptive VSync from NVIDIA Control Panel not with VSync in game.
But you describe freezing on some moment and that's not good. Normal card shouldn't behave like that. Did you check voltage on PSU maybe?
You can do that with Molex connector and voltmeter during full load, 5V and 12V rails.

psu is a new one. tried now older drivers and that made it more worse.

It's very bad politic of NVIDIA, maybe they sabotage and GTX980 performance to force people on GTX980Ti.
Do you know what mostly influence bad on me when I think on TITAN X... Fact that Hawaii is stronger than GTX780Ti and TITAN Black and soon will be stronger than GTX980 because NVIDIA drivers...Such problems force me in complete opposite direction than NVIDIA plan. 
 
No excuse for such things, for every mistake they need to face with same things as with GTX970 false advertising. 
Many people will pay much earlier if they notice how older cards work good but they need more performance, not less fps because NVIDIA drivers and because NVIDIA don't want to improve performance or 1 year old card for new games. 
Maybe is solution for you to send card to EVGA or step up on some more powerful.

Ok so this one might be too easy , but go into the nvidia control panel and under manage 3d settings go down to Vsync. Do you happen to have Adaptive(half refresh rate) enabled?

We also tried the graphiccard from my friend (R7 260X) to see if there will be a huge difference . there wasn't much different you could say it mostly was the same when not be a bit better, and let's say, that shouldn't be because the gtx980 should be much more powerful.

we done all this, and thinking about changing back to amd graphic card or change mainboard and cpu to intel, graphiccard would be cheaper.
we have enough from searching what the heck is going on with the system/graphiccard/cpu

yes we have

so we done another benchmark, that gigabyte support suggested. stutters, micro stutters and framedrops down to 8.