I been playing around on a test server, here is my favorite Megathron fit for solo or small gang warfare:

[Megathron Plate + Ion + 2xnuets]
Magnetic Field Stabilizer II
Magnetic Field Stabilizer II
Energized Adaptive Nano Membrane II
Energized Adaptive Nano Membrane II
1600mm Reinforced Rolled Tungsten Plates I
1600mm Reinforced Rolled Tungsten Plates I
1600mm Reinforced Rolled Tungsten Plates I
100MN MicroWarpdrive II
Heavy Capacitor Booster II,Cap Booster 800
Stasis Webifier II
Warp Disruptor II
Modal Mega Ion Particle Accelerator I,Antimatter Charge L
Modal Mega Ion Particle Accelerator I,Antimatter Charge L
Modal Mega Ion Particle Accelerator I,Antimatter Charge L
Modal Mega Ion Particle Accelerator I,Antimatter Charge L
Modal Mega Ion Particle Accelerator I,Antimatter Charge L
Modal Mega Ion Particle Accelerator I,Antimatter Charge L
Heavy Unstable Power Fluctuator I
Heavy Unstable Power Fluctuator I
Trimark Armor Pump I
Trimark Armor Pump I
Trimark Armor Pump I
Drones_Active=Ogre I,5

Has over 100000 effective HP. In tests it took over 90000 in damage before going down. A Megathron setup with 2xLARs lasted only for 40000-50000 damage and had also problems with cap.

Setup created in EFT. You can copy paste that in your Megathron.cfg file or create a new one.