Thanks for pointing out that link Martin, one I hadn't seen. Yes, it gives a formula for the resonant frequency corrected (effectively) for Q. Applying that with Q values of 3000 and 5000 gives corrections of 3.3 nS and 2.5 nS respectively! The simulation results can't really be relied on to nS periods because of the way it calculates periods, but in mechanical clock terms the difference is irrelevant. The difference is 0.8 ns per 2s, which is 3.5 ms in 100 days.
Somewhere I have seen that the impulse from a deadbeat escapement (such as the Graham) is slightly imbalanced, that is it's slightly off-centre from the pendulum swing. This means that the impulse is slightly out of time phase with the pendulum velocity, resulting in a small time error. If the impulse phase is in advance of the pendulum it speeds it up; if behind it slows it down. The imbalance is geometric, but the amount of resulting phase shift depends on the pendulum amplitude. Suppose the imbalance is slowing the pendulum down. You add a spot of oil, reduce the friction, increase the amplitude, reduce the phase shift, and the pendulum speeds up.
You asked about the circular error at working amplitude. The fractional reduction in rate is just (amplitude in radians)squared/16 assuming no correction. At 1 degree, or about 1/60 radians, this is 1/(3600×16) = about 35 microseconds for a seconds pendulum. This is exactly what the simulation gives as well. You can scale up or down from that for other amplitudes.
Air resistance law has to be specified in advance, linear or square law. For normal amplitudes of a degree or so it seems to be about linear, but at Harrisonian amplitudes of more like 6 degrees it's probably square law.
Your last paragraph –
"Just as a thought all this would indicate that Harrison thought a great deal about the effect of drag on the action of his pendulums and although I have no evidence to prove this, maybe thinking about the shortfalls of Graham's clocks lead him to understand the effect sufficiently to use it (as atmospheric drag) balanced out with controlled circular error to create a system which was largely immune to atmospheric changes."
– there seems to be no doubt that this is exactly what he did, though not just circular error but escapement error too.