I will not claim to have understood what has happened.
I only think that your best source of information on that subject is the TBP team. Why? Well, because if you come to think at the time they took incorporating all those ships on TBP, well they should know what works, and what doesn't. How to fix it then, should be easier. My gut feeling has to do with the amount of faces in the shield, AKA when they are lower, the game should be more stable, but then that is all I can think, right now.
I am watching this project and honing my skills to help as a Freder. Good luck with the ships.