i have a similar issue, im perfecting my ss build for the playthrough so i havent really gotten to ACTUALLY PLAY the game in weeks, other than some very short playtesting and making sure my recording setup functions properly
from what i have done so far (keep in mind i only tested the original upload, so i dont know about it since your changes) they are just fine and not OP at all [now i didnt test every weapon, just the two biggest ship and the missile destroyer/ it has a single large hybrid(?)] and SOME of the weapons: in particular the small laser cannon and the medium flak (I F***ING LOVE THAT FLAK GUN AND THE LASERS ARE GOOD TOO, however, not sure that the twin laser should have built in pd capability. being that it is a main damage dealer i found myself somewhat annoyed that it wasnt focusing fire on ships)
i would say they are just fine and will fit in PERFECTLY in the modiverse (please remember i essentially have every mod from the community enabled. no, i am not kidding)
there are A LOT of ships in the modiverse that provide PLENTY of challenge for your ships.
a good example would be pulse industry that just dropped an update for 95: they have a super capital ship that is essentially a mobile station
speaking of mobile stations there was a mod for .91 that literally just made stations pilotable (top speed with boost is 60; on average they move more like 5 su so its perfectly fine. i really hope that mod doesnt die. i would love to have a mobile star fortress fleet that functions as a colony on the move)
well, thats not entirely true that creator did more than that there were also some cool variations
anyway in my opinion i wouldnt nerf them at all. there are PLENTY of mods that far outclass your ships on a ship by ship basis, even though they are quite powerful.
HOWEVER they are definitely onpar or perhaps better in many cases than the most powerful vanilla ships, just at a glance anyway i havent done in depth testing.
NOW that that is out of the way, PLEASE DONT NERF MY BADASS SPACE BATTLESHIPS!!!!!!! lmfao thats my opinion.