I salute your goal. Hopefully you can also add enough new ships to make bounty hunter mode interesting.
Based on the displayed numbers I suspect that component damage is deprecated and structure damage is used instead. The plasma projectors and iridium lasers feel very weak against unshielded targets compared to what their stats suggest.
The range increases need to include an increase to base detection range. If any weapons that do not require an advanced detection part have ranges exceeding the base cockpit detection range NPCs with those weapons will not use them at their full range even if being shot at. This is a problem at least with missiles.
The cruiser bridge has asymmetrical doors, which makes it work poorly with mirror mode. It really needs a second door at the back. The Warp Core Engineering has the same issue. It really needs another door at the back since it's really too big to build around without a decent door distribution. The Weapons Control has the same problem and would actually work better with the door arrangement of the Tactical Center.
The bridges in general work poorly. The crew AI has a hard time keeping any component that requires as many crew as even the frigate bridge crewed consistently, meaning that a basic command center is practically required anyways. I'd suggest using rooms that only control weapons as your tech buildings.
Ion and standard missile launchers are indistinguishable in blueprint mode. I also suspect the Ion Missile will be too powerful against shield builds. Missile explosions already pass through shields, but a shield build that accounts for that can do will until it closes to electrobolt range. I expect that a mixed ion/explosive missile armament will be even more overpowered than missiles are in stock.
The two capital turrets have angle problems. So, to a lesser degree, does the iridium laser. A weapon must offer more than 90 degrees of arc to be viable on diagonal builds, preferably significantly more. Stock cannons with different facings have 50 degrees of overlap. The Iridium has only 20. The Vulcan and Assault Battery have 16 degree gaps. They also seem to have more power draw than can be fed through their limited doors.
The Iridum laser passes through shields. Passing through shields is a very powerful ability and there's a reason only the shortest range weapon in the stock game has it. It can be used to snipe surface components through shields. Especially if the damage to structure is raised it should lose shield passthrough. Also, Iridium lasers have explosion GFX but the Plasma Projectors do not. This contradicts the descriptions.
LFC shells need particle effects. They're currently nearly invisible. They also feel a bit anemic compared to stock large cannons. I suspect it's the lack of firestarting. Without firestarting damaged internal components have no effect on the ship without multiple hits on the same path.
If you're going to have engineering rooms unlock stuff, you should probably have larger engines tied to them. And possibly a space warping drive based on the warp room that can be placed internally.
The value of laser PD over stock PD is dubious. The damage to non-projectiles is not realized because they only fire at projectiles and if they did fire at ships they wouldn't have full charge when needed to fire at missiles.