Short version:
Initially: RV6 (2002), over 2000 hours with a carbureted Lyc O-320 [conical mount] and Hartzell CS prop at the end. One Jeff Rose EI and one P-MAG. Ran smooth. No issue.
Side note my RV-4 had similar set up. It took Lord Conical Mounts and a good Prop balance to get it smooth. It was not like your current situation, but no low RPM shutter just high vibration levels all the time.
You now have new engine with Dynafocal mounts or your original O-320 with conical mount? If you don't have LORD mounts regardless get them. If you still have conical mount... GET LORD MOUNTS TODAY. That might solve it.
Now: Fuel injected (AFP) 340 "Stroker" + Whirlwind 200RV prop.
This was a 320 up to 340? There are 340's which are low compression 360's. So a "stroker" does change the vibration harmonics by itself. The prop is also experimental. Once you modify engine, stroke it (not a certified configuration) and put non certified props on that non certified engine, with non certified EI possibly, you have a very experimental system. Certified props get flight tested extensively with strain gauges and vibration measurements at all RPM's and MAPS. It is possible you are going through some transient harmonic vibration mode. Does this happen on ground run ups?
What little I know about Whirlwind 200RV I assume it is similar to a MT, wood blades with composite wrap and metal leading? The blades should be very vibration tolerant, and resistant to fatigue. The hub is metal and of course subject to metal fatigue. I would not think the HUB is the issue in shutter? Usually the blades themselves mostly vibrate not the hub.
Did you talk to the Prop maker? Call or write them with details of everything and ask if vibrations might be an issue.
Issue: When I pull back on the throttle in flight there is a "shudder". Think reducing throttle for landing. Think adjusting throttle in formation.
When RV's pull back power abruptly can get back fires and protest from the engine. Possible it is really shaking and vibration is transmitted through baffles hitting cowl and engine mount. Vacuum leak? You state you checked the induction tubes? Ignition may be involved? Do you have magnetos or EI?
What if you pull power back really really slow? You should avoid abrupt throttle changes and Lyc states that in their technical data. Worse are counterweight cranks and engines with gear boxes which you don't have.
Prop and FI systems have been removed and verified as in good working order by Whirlwind and AFP. No apparent induction leaks.
ANY IDEAS as to what MIGHT be causing this? I have bounced this off many people but no solution yet. So I appeal to the vast warehouse of "all things RV" knowledge.
Just hanger flying no brainy idea.
> Lord Engine mount vibration isolation, especially if Conical
> Balance prop again (I had to get mine balanced twice, the first guy was not good, the second balanced helicopter blades and world of difference)
> FI has been checked but make sure no induction or vacuum leaks
> Ignition wild guessing