Sorry I realise that this is over a month old but my cousin had a similar thing happen to his rm250 recently after he changed the pipe on his bike and didn't bother to tune it. It caused the same symptoms as your bike, with the bogging feeling being caused by the piston expanding too much and trying to stop in the bore, and the same marks appeared on the head from detonation or pre ignition(I don't know which is which). If it were me I would check everything to do with the coolant, combustion and timing in the engine, including the compression and doing a leak test once it is reassembled.

I notice you had the head milled and port work done...maybe the compression ratio has been messed up.