In the FOS cylinder there is a stable axial scavenging column (
http://www.kiwibiker.co.nz/forums/sh...post1130452977) centered in the bore, rising up until it collides with the cylinder head.
This collision has two effects. There will be a pressure rise in the head which will slow the flow down; the pressure inside the rising column will rise and the column will expand in diameter, pushing the spent gases that surround it, into the four exhaust ports surrounding the bore.
The second effect of the collision is that the axial column mushrooms in the head and flows down along the walls of the bore, pushing the spent gases that were clinging onto the bore, towards the exhaust ports.
In a conventional cylinder this axial scavenging column is supposed to cling to the rear bore wall. This clinging gives it extra stability and at the same time helps to scavenge the spent gases in that rear area. If the rear transfer port doesn't have that upward angle, it has much more effective area, as you say, so the flow exiting from it can be so much stronger that the axial scavenging column doesn't get a chance to cling to the rear bore wall. The spent gases in that area will no longer be washed out and they have nowhere to go because unlike in the FOS cylinder, there are no exhaust ports in the rear wall of a conventional cylinder.
So although this better-flowing rear transfer port may bring more fresh charge into the cylinder, it may also cause less-effective scavenging, leaving more hot, polluting spent gases in the cylinder. The net result may be positive or negative, depending on your cylinder layout.
Jan Thiel has tested every imaginable port configuration and the Aprilia layout as we now know it was the end result. But things may well be different in your cylinder.
I'd say: reduce the axial angle of the rear transfer port until it does not improve power any more (it will certainly improve piston cooling). And if you overdo it, you can easily increase the axial angle again with some epoxy, or narrow the rear port, which will have a similar effect.
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