I have a similar problem with that on my newly built PC, even though my system is well above the recommended requirements, yet on my older lower spec machine, it runs great, same mods, same save, so I can rule out any of those suspects. Mine been like lag spikes every 30 seconds, 30-40 seconds of perfectly smooth gameplay then the screen will freeze up completely for 3-5 seconds only thing that's isn't affected is the audio that continues as normal.
I can rule my problem to be either an OS/Driver/Hardware issue, so first thing is to keep your graphics drivers up-to-date. Hasn't helped me yet though, but lately I have noticed a squealing sound coming from my GPU during the freeze moments, suggesting the CPU and GPU are bottlenecking. I might have a decent CPU and GPU but when they work together their timings seem way off.
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