Ouch. So with the round ports and oval runners having the same cross sectional volume you will be forced to both grind from some spots and add material to others in order to avoid a flow restriction. Any sort of smoothed angles would help but I'm not sure how much in that short of a distance, particularly where the air temporarily stops to wait for the valve to open. I have had a great deal of success in the past when maintaining volume while changing duct shape but it has always been over a much greater distance to avoid turbulence. The airbox in this picture from one of my old posts is a good example.
http://club-s12.org/retro4/index.php?topic=33597.msg349240#msg349240On the far side (where you can't see) a 3.5" round duct enters a tapered square cone that gradually flattens out into the rectangle at the top of the engine. After crossing it squares back out into that complex angled box that acts as a funnel into the 3" supercharger inlet. After dedicating a few days to measuring, cutting, bending, riveting, and starting over we came up with that design which at all points that funnel-to-box-to-funnel has the same volume as the duct at either end. The flat box was required to fit under the upper cowling of the aircraft. We did full power tests on the ground using smooth aluminum tubing and found no appreciable difference in velocity entering the supercharger or pressure exiting it. Unorthodox but it was and continues to be highly effective.
Ideally you would test with both complete UIM/LIM combinations, then retest again with both of your hybrid options to tell what the difference is. Testing like that is always time and cost prohibitive though even if you already have the sensors and testing equipment. Not to mention really fucking lame compared to spending time driving. You might also use the intake side head gaskets as templates to create two plates and the LIM-to-UIM gasket to create a third. Then you could use tubing to link them together creating your own LIM. It would be time consuming and costly (and you certainly have other items on your list to spend time on) but it would solve all of those issues. Tricky issue anyway you go. Still looking forward to all the updates between now and then whichever way you go.