OK, to give an idea of what I'm talking about when I run into issues, here's a slapdash transport/bomber version:
Karnov AutoMek
Base Tech Level: Experimental (IS)
Level Era
------------------------------
Experimental -
Advanced 3070+
Standard -
Extinct 2865-3040, 3085+
Tech Rating: E/X-X-F-F
Weight: 40 tons
BV: 1,147
Cost: 3,585,493 C-bills
Movement: 4/6/6
VTOL: 9/14
Engine: 160
Double Heat Sinks: 10 [20]
Gyro: Standard Gyro
Internal: 67
Armor: 96/137
Internal Armor
----------------------------------------
Head 3 9
Center Torso 12 12
Center Torso (rear) 5
Right Torso 10 10
Right Torso (rear) 5
Left Torso 10 10
Left Torso (rear) 5
Right Arm 6 10
Left Arm 6 10
Right Leg 10 10
Left Leg 10 10
Weapons Loc Heat
-------------------------
Medium Laser LA 3
Medium Laser RA 3
Medium Laser CT 3
Equipment Loc
---------------------
Cargo (2 tons) LT
Cargo (2 tons) RT
Speed taps out at 9/14 in VTOL mode, with 4 tons of cargo. Dropping to 4/6/4 base would make it 6/9 in VTOL mode, and add another 4 tons of cargo.
That's not awful, I suppose, but I'm still not sure I'm going about it the best way here building VTOL AutoMechs.