That first group of terms (including the compressor and low-cut filter) is pretty standard audio theory which you can find on any modern sound board.

As to your resonant frequency discussion - I would think that it's the ringing of the components you'd be most worried about, particularly the crankshaft. I doubt the piston would ring at all; perhaps the rod, but it'd be more likely to ring laterally than longitudinally? (I'm guessing here). The crankshaft is the part most likely to deflect and resonate because of a sudden impact. Any resonance inside the combustion chamber would be at the speed of sound, resulting in an extremely high frequency with such small dimensions and low mass (of the air).

BTW I appreciate your thoughts towards changing resonance. I went down the same road over the past year preparing a forged stroker motor and finally decided to modify a Fluidampr to fit my B-body setup, since it is an effective multi-band damper. The stock elastomeric damper is a single-frequency damper; ATI is also single frequency but it is tunable (by ATI), though I don't know how one would get data back to ATI. So... I waited for a long-discontinued LT1 Fluidampr to show up on Ebay and then modified it and my accessory drive to work on my application.