2003 RM250 head mod

Opening up the combustion chamber may not matter. The ignition maps on late model 250s are real aggressive and it can't even be compensated for by retarding the stator plate. Have you tried a richer needle or bigger power jet? That may be all you need. The power jet is active in the mid-range. Another potential problem is that the solenoid that drives the power jet may not be working. You can test it with a multi-tester, it should show 5VAC when the throttle position sensor clicks on at about 1/3 throttle. You can also remove the sub-frame, start the engine and just look to see that fuel squirts out of the jet when you roll on and off the throttle.
Remember AV gas is low octane (87-89MON) but the lead content should reduce detonation but maybe not enough. That fuel was made for 4-stroke engines that run at high altitude which also implies lower air density and cranking compression.