I am unaware of anything within a 4 cyl opposed engine that would
theoretically that would give anything at the 3.5 harmonic. I think
you might be looking at a non-linearity in the mount (is it a dynafocal
or a straight conical mouint?) or in the transducer(s) mounting.

I'd guess the 3.5 order output to be comparatively insignificant
compare to the 0.5 harmonic as far as human discomfort is concerned.

Do try the prop indexing thing. Let us know the results.

Good luck & THX