Looks great Keith!
Only a few comments:
Heavy Bomber Starships have the same Cap Health as the Zenith, but no bonuses, and they can't hit the majority of ships in the game...literally. Their speed is nice, but is fairly useless in a fleet, and for raiding, Raid Starships are much more...ideal to say the least.
Before, Heavy Bomber Starships were good against Guardians, but now that most Guardians have the "Medium" Hull Type, Fighters counter them very well, and are astronomically cheaper. Which essentially leaves buildings and shields, which the Bomber Starship only does so-so damage against. In other words, I think its DPS needs to be as high, or even higher than the Spire Starship's to compensate for its poor range and severe lack of targets it can hit.
At least, I won't be building them until that happens.
In addition, I don't think the 40% DPS nerf on the Siege Starship is warranted. If they moved at normal Starship speeds then that would be fair, but considering they are the slowest unit in the game, I don't think their range or damage should be nerfed to compensate for their new durability. Personally I'd rather you just up their speed than keep their damage, but it's your choice.