The data saved with it this time is for a passenger/freighter ship with enough just about enough range to reach Titan from Earth.
Going down the page, the type of atomic blast determines its efficiency - Uranium blasts are cheapest and least efficient, but have minimal running costs since they use salt as fuel. Protactinium is best but hideously expensive to run, since the fuel is lead.
Emergency acceleration is normally used for a few minutes at the beginning and end of a flight; cruising acceleration is used for weeks on end, and is much more efficient. The higher either is, the more the engines costs and weighs, but the major factor is emergency acceleration. A racing engine can run at emergency power for much longer without melting / exploding, but you pay a hefty premium in weight and costs.
Flight duration determines the mass of supplies you need per trip - e.g. oxygen, water, food. You have to build for the maximum journey planned for the ship, e.g. a trip to Mars is just under two weeks at .03g, Titan is 68 days at .015g
Ships that are equipped to fly and land horizontally (like e.g. a VTOL aircraft) are better for military use and exploration, but add a lot to the cost of the engine, plumbing, etc. Most ships take off and land vertically, which makes it much harder to control your precise landing point.
An algae "farm" is most useful on long flights / big ships, it's heavy and expensive but reduces the other supplies needed by a third.
The rest should be fairly self-explanatory, I think.
I think it's moderately bullet-proof if you don't disable protection, let me know if I'm wrong. If there's anything you don't understand please ask below.
One thing - I haven't tried to have fuel tank size determined by flight duration since there's a circular argument in there - the best way to work it out is trial and error. It's VERY hard to build big fast long-range ships.