I have this problem in which the game stops for more than a sec and then resumes. This happens every 5-10 minutes. I'm quite sure this has nothing to do with the hardware nor with modding because it only happens in a certain save while in the others nothing happens and everything plays fine. I could load another save but the problem is that I've progressed too much compared to the other "corrupted" one.

How large is this save file, and how many hours played?

@SomeWelshGuy it's 53kb and I've played for 140 hours

53kb?

A save straight out off the cart at Helgen will easily be at least 2-3MB. Perhaps you should check again

oh sorry my mistake 53 MB

If that's the case then that's a massive save. As a comparison, I've played 100 hours on this character and my save is 8MB in size.

Have you removed mods from your game and continued to use the same save? You have massive bloating issues and that's what's causing the game to stutter and for performance to generally be poor.

You can try the console command ClearInvalidRegistrations with the latest version of SKSE enabled, and your save may reduce in size over time. However the only other option is to really use a new character as your current one will become severely unstable soon, and be careful to not remove mods from your game mid character.