I'm including as much information I think could be relevant to give me the best chance at a working solution so I will include a tl;dr at the bottom.

The problem:
Upon launch the video and ability to give inputs with "freeze" for a moment every few seconds at a fixed interval. Sound continues as normal. I thought it was something I could just play through but the lack of ability to input when it "freezes" makes gameplay very uncomfortable/unplayable in moments of higher actions per minute.

Relevant computer specs:
OS: Win 7 64-bit
Processor: AMD FX™-6100 6 core ~3.3GHz
Memory: 8G
GPU: AMD Radeon R9 200 Series

Things I've done to try and solve the issue:
-Updated GPU drivers. Yes, this includes the new (as of Nov 18th) beta drivers. Yes, this was a clean uninstall and reinstall with restarts and all. I know that AMD plans on doing a new batch the 22 or 24th or something but I am hesitant to believe this will solve my issue considering the recent batch (meant for Fallout 4 issues) didn't.
-Tested with older GPU drivers.
-Playing on the lowest possible graphics settings (though my machine should be able to run ultra :/).

I searched forums for similar problems and am coming up with nothing. I find it hard to believe that I've stumbled upon a completely unique issue, but...maybe?
Any help welcome. I would even play at the lowest graphics if it meant I could do without the constant pauses.

Promised tl;dr: Game “freezes” at a consistent rate every few seconds. Have a machine that should handle game on ultra with updated drivers. Would prefer if you read “things I've done to try and solve the issue” before making suggestions but I don't mind repeating myself if it means I get to traverse the Bostonian wasteland.

What is the specific GPU? There are several R9 200 series cards.

Ah, I'm so sorry! It's a 290X.

There are numerous posts on the forums about this, they call it stutter.

It appearantly originates from the "enabled controller" in the game.

While in the game, go to settings, and disable controller.

And i recommend taking a look at this link. Helped me out a lot.

I had all these problems too and i just followed step by step on the tweaks in the link below, and it cured everything for me.

http://steamcommunity.com/sharedfiles/filedetails/?id=551069501

I belive most of what you experience is from FPS cap. You probably got struck by the same version i have which is hardcapped at 30 FPS.

Now if you unlock the FPS cap, the game will not function correctly if you dont cap it between 60-70 FPS your self.

I ran at 140-600 FPS on ultra to begin with... but my gun kept disappearing visually... i got stuck in hacking terminals.. lockpicking was running at 2000 FPS so it was in SUPER fastforward, so as soon as i touched a button it breaks a bobbypin. etc etc... even running when the FPS spikes, made me walk super fast...

so use a software or something to cap the FPS to around 60-70 and you will notice a BIG difference..

The other tweaks too are quite awesome.

Personally i loved the removal of death of field.

Oh my goodness, I can't believe how easy it was. My googlefu/searching needs work; I feel like I searched all over with nothing! Admittedly, I didn't know to look for "stutter". Still, thank you so, so much!
It was disabling the controller, btw, that did it.
Seriously, so happy right now!

Happy to help