I dont know if theres anything you can do in your current save, other then just removing some excess items. The only "fix" I can think of is to remove things from the Zidrom itself, like some exterior lights, or excess items. There are a few different versions of the Zidrom on the workshop. Im not sure how different or even better they are when it comes to fps issues!
But Ive had alot of comments on fps issues and the sub has gotten better over time due to the developers improving the game and some quick fixes on my end, but at the moment without completely changing the size and amount of "things" on the Zidrom, theres not much i can can think of that might help you!

Ah damn that's unfortunate the ship is honestly super cool but not really playable with the fps issues for our save anyways. Oh well hopefully baro eventually fixes the issues because I think most larger subs have this issue to varying degrees. Thanks for the reply tho.