I understand the trouble you are having tuning with methanol and the supercharger... It is not for the faint of heart, but you can do it if you understand most of the major issues....
Methanol burn rate is slower than gasoline (18% to 22%), so all else being equal, you need more spark advance so peak cylinder pressure occurs at the sweet spot of the power stroke (10 to 15 degrees atdc or so).
Boost pressurized fuel mix burns at a faster rate than normally aspired mixtures so you need less spark advance to get the cylinder pressure at the power stroke sweet spot....retard about 1 to 2 degrees per 5 psi boost is a good starting point
Yes, they tend to offset somewhat with the methanol burn rate being the major effect .
Boost mixtures become harder and harder to ignite due to the insulation effect of nitrogen gas, so spark plug gaps have to go down.... .016" to .018" at very high boost or with a weak ignition system.....
Methanol will detonate when pushed to it thermal stability limit... It is about the equal of 116 octane gas when it is good ,,, a lot less when lean...
A/F GAUGES usually don't read accurately when methanol is rich,,, use the EGT instead.
Timing should be set for "best continuous torque" in the power band of the engine... Setting for the peak output using an inertia type dynamometer or short sprint runs has killed more endurance type racing engines than saints in heaven .... When one is WFO for more than a few seconds at a time,,, the tune must be turned down else killer detonation will occur...
A "Knock-Sensor" system would be your best friend in finalizing your tune....
Good luck and I'll continue following your efforts with interest....I have a air-cooled blown 350 pushrod motor that is also very tricky to tune....
Robert in California