I have my ignition amplifier bolted to a large piece of aluminium to act as a heat sink for it. Unfortunately, the only convenient place to mount it is bolting it to the cylinder head, which I think is going to shunt heat into the amp rather than away from it.
Are there any sort of washers I could use to reduce the heat transfer from the head to the sink?

Ceramic washers?
Hope you've got some air flow over that amplifer if you're doing that! The ambient temperature around the h/sink is going to be huge!!
Personally I'd find a different place to bolt the amplifer. Other than bolting it directly onto the exhaust header you really couldn't find a worse place!!!