Erik,
Question about the Engine Tech tree, I would expect the higher tiers of this to have pre-req's of some of the Energy tech trees; for example Engine Tech V (Plasma Torch) you can develop these as N-space engines even without beginning on the Plasma Tech tree. Engine Tech VII is the same not requiring knowledge of Fusion Tech.
Admittedly it will make the tech tree a little trickier and will make things like, Fusion Tech pretty much requires Plasma tech as a pre-req if you want to develop the Engines. gameplay wise it's not going to be any advantage to do what I'm talking about, it just seems weird to me that I could theoretically have Anti-Matter Pulse engines, but have never researched Antimatter Tech.
Actually another way of doing it, the names Nuclear Pulse, Plasma Torch etc are really just flavour, so maybe making the engine names more generic, or using different names not tied in so closely with the reactor tech's would be a thing.