Simply take two Hangar Doors opposite to each other - that will give you 4 large blocks of space in height, enough for any decent craft.
Btw, i tweaked your craft a little to make passage in and out of atmosphere possible and redid the conveyor system to breathe air inflight :)
I´ll upload it in a few minutes so you can have a look.

Thank you. I'll try to rebuild a new proper aerospace fighter. One problem i find is vanilla hanger doors are quite low and I don't want to use any mod ones

Ps: The Cockpit is not properly conveyored so oxygen cannot flow.

Insufficient Atmospheric thrusters to fly in earth-like planet atmosphere (survival).
Tried today, even with no cargo (ammunition and stuff) AND ion thrusters turned on to assist the decent, the ship was unable to brake in time.