More flywheel inertia is an absolute good for torsional behavior, as you've now seen for yourself. It will, however, add one oddity in the case of your Marcotte gearbox, which rotates the prop in the same direction as engine rotation. The additional inertia will add to gyroscopic precession. I think you'll notice the difference, although it should not be a big deal with the 6A. My scaled JN-4C (or an original Camel) was more interesting because engine/prop inertia was much higher in proportion to airframe mass.
An ideal PSRU would rotate the prop opposite the engine so the prop and flywheel gyroscopes offset each other. In theory you could have less precession than a Lycoming.
I'd read about this fact on EPI's site but forgotten about until you mentioned it here again. I'll watch out for it and see what I notice. For the time being, I am very pleased with the change and this mirror's the experience of two others who switched to heavier flywheels on the Marcotte. Once I get further along in testing and have some time, I want to wade into the MOI and stiffness models. Still very interested in what could be happening further up the rpm range.
I will do some more testing on the cooling system today as it should be warmer today.