[Tinman]

Your hyperdrive size problem & other issues could be easily solved by building your ships with GURPS Spaceships. Have you considered using that?

I've used the Spaceships books to design spaceships, age of sail ships, Zepplins (as mother-ships for for fighters) & other types )including as a flying base for my DF Artificer & his party). It's a very versatile & simple system.