Now going full on "Illegal" and using an internal LAM Bomb Bay, you lose an RL-10, but gain a LOT of flexibility and and quite the discount (59,740)...
F-5E (External stores) Tons Cost
Tonnage 5 0.025 Multiplier
Engine 1 2,083 25 5/8 Thrust
VSTOL 0.25 1,250
SI 0 20,000
Fuel 2 400 320 points
Armor 0.25 2,500 1 point everywhere
Avionics 0.5 2,000
Attitude Thruster 0 25,000
Landing Gear 0 50
Internal Bomb Bay 1 5,000 Illegal (only for LAMs per IO)
Sub-Total 5 58,283
Total 59,740