So, I've re-balanced your ships as you requested, following your instructions. I'm done already as I managed to start before Thursday.
I haven't included the ships you told me not to touch. That way you can just use my folder as your new version folder and plop the ships you told me to leave out into it. This should prevent you from accidentally missing anything when moving ships or something. I figured it would be the easiest for you, and decreases the odds of you missing something.
You don't appear to have standardised PD, with only two types of reoccurring turrets and the rest being whatever you set it. As such, I didn't follow any standardisation either and simply changed the values as I thought worked.
I've also done one tiny little change I forgot to mention in my list but was planning to do anyway: I decreased the submunition lifetime of Particula-M's mines that so that they don't scatter over such an ENORMOUS area as they did before.
Other than that mine thing, everything is strictly by the list and your instructions.
Necron, please include all the sprites you use on your ships in the OP.
For the ships you're rebalancing: I strongly recommend you don't give Atheist a photon lance stronger than Frequency 1, and instead put more secondary weapons.