The Prowler gearbox seems to be a stiff solution. It does not appear to have any quill at all. Astonishingly the reduction is bolted to the FRONT of the engine, thus eliminating the harmonic damper. The accessories are located on the normal PTO side of the crank. This makes the prop turn in the correct direction, but good grief! I can't see how there aren't problems, but seems to work!
Using Billski's method of 2X the operating frequency would seem to favor the stiffer solution as long as the lash in the gearbox and the weight of the prop doesn't bring things down into the operating range. Fortunately most sane aircraft conversions with a gearbox keep the revs reasonable ~4000 rpm. So the primary frequency should be >2200 Hz for the gearbox case.
In Toobuilders direct drive case, operation should be around 2500 rpm so the primary should be >332 Hz (I calculated this by multiplying 2xRPMx(4 firing pulses/rev)/60s/min) This isn't exact, you need to look at the firing order, I'm just doing ballpark here. IIRC the V8 is odd fire, so you will have even lower frequencies.
YIKES! Direct drive results in low frequencies. If you are trying to push your resonance below idle.....I'm not sure how well that is going to work out.
It would be interesting to "ring" the prop and see where the blade resonates. I used to have a spectrum analyzer program on my pda. Surely there is one for the iphone.