Sorry to ask again, but can anyone familiar with Spacecraft 3 look over my script and get this thing to fly right?
I have no huge experience with spacecraft3, but I can do sanity checks on the physical properties.
is already a pretty bad choice, since you have no winged vehicle and a pretty strong VTOL components in its flight model.
7200 kg is not 2.5 tons - Orbiter uses SI system, not imperial or US customary.
fuel mass is a bit low with 440 kg, but you can compensate this with specific impulse. Specific impulse is measured in N*s/kg in Orbiter - your value of 578594.4 means: Each kg fuel you burn, results in 578594 Ns impulse, Impulse = Force * time (roughly) So, each kg of fuel of your spacecraft results in 1.57 seconds full main thrust. All together just 692 seconds. Not that bad since you rarely should fly at full 5g - at one g, you would fly already for one hour.
Your attitude thrust is a bit high. 39000 N is damn strong, one percent of this would still be strong for a spacecraft of your size and weight. Your PMIs are also a bit strange, maybe you should run them on shipedit again and let it calculate better values. Your attitude thrust would result in the spacecraft rotation accelerating at 101°/s²!!! Even just tapping the key would result in about 10°/s rotation. Almost impossible to have accurate control with that.
EDIT: Correction... did not look at the size parameter, your size is 9.6m, not 3m as I wrongfully assumed. Your rotation acceleration is thus over 300°/s².