Seems like that's the only way to squeeze it in there with the powervalves, I wonder if there are existing engines with a similar configuration?Looks like exhaust has a Transfer type porting, Goes out, down then out to manifold. No way it would run being that low.
Although...the PV blade would have to be right at the edge of the inner bore to effectively change port timing sooo..drawing a straight line down from the center of that PV bellows would put the blade (and therefore the port window) lower in the cylinder than you would expect it to be. I'd say to work with the valve, it would have to be a straight shot runner from port window to manifold, which would make it very steep and give it an odd cross section.
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