Lightning and auto pilots

[the dude abides]

I had a direct hit by lightning on my VHF antenna. It has fried a few things. AIS, VHF, SSB, Gas Stove monitor, Camera up the mast, Wind instruments, Charger inverter, gas stove monitor, pac modem, back up chart plotter and auto pilot.
I am insured but it is still within my interests to keep costs down as I am cruising in South East Asia, I am not working or generating an income.
Big cost item is the autopilot. I have a ST6000 autohelm, an oldie but a goodie. The control monitor works but when I press the auto is quickly says low battery. This means it is registering under 11 volts on the battery, which is incorrect. Course computer fuse is fine, circuit breaker is working like it should, the control monitor appears to be working but reading low battery, so through the process of elimination, it should be the course computer itself has been compromised.
I have been told though by some people, replace the lot if it has been hit by lightning. $4.5 k for a auto pilot. $400 for the course computer. I pay 30% but as you can see there is a lot to replace and I need to keep expenses down.
So the question is do I just replace the lot, or just go with replacing the course computer. I know I could try one and if it does't work try the other, but the insurance company processes the one claim.
Anybody out there that has had a similar issue with lightning and autopilots? Attached is a picture of the bracket where my VHF antenna used to be.
Cheers everyone.