Hello, I'm loving this mod. I haven't played Starsector with mods much largely because everything looks out of place next to the stellar vanilla artwork, but your ships fit right in both mechanically and aesthetically.
For your phase cruiser, why not some variation of the burst thrusters you can use in phase cloak? Coast up to your target while phased, burst jet through him and turn, then unload. You could make it slower than the Doom to compensate, or give it a decent flux cost to make it tricky to pull off without overloading. Alternatively, I like using the 0-flux boost and/or maneuvering jets to get to high speeds then coast past enemies and do strafing runs, allowing me to vent safely afterwards; you could have a system like the burn drive that doesn't throttle your speed down when it's done, allowing you to do high speed, difficult to target bombing runs. I don't think the AI would like that one though.
I've been thinking that it would be interesting to have ways to weaponize flux. For the Sachumodo, instead of having it activate at 0 flux, perhaps you could make it so it deals damage proportional to the amount of stored flux and overloads.
Finally, I have to know, because it's been driving me crazy: what the hell is the Lucifer generator?