More cones and more measuring distance between plenum cover and top cowling. As I finally got satisfied on the compromise everywhere between 3/8 and 1/2 inch overall and some places slightly over  1/2 inch, I started drilling some pilot holes #40 on the left and ride side. As you see in the image, couple of holes left and right at front and aft of the plenum. After drilling the first holes, repeated the measuring process. I am probably overthinking this, exagerating  and loosing to much time but if you know that shipping the cowling costed 250$ + 8% import tax and on top of that 21% vat, you probably understand why I am very cautious about every hole I drill.

Below it the image with the holes drilled.

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The height of the plasticine cones is close to 1/2 inch left and right on the diffusers.

 Continued then by drilling the full row of holes to #40. The baffles on the side are still way too high and will have to trace and cutback.

I slightly moved the rear pilot hole a bit up but this will be invisible once the hole get's updrilled for a #6 screw. 

 Here is the inside view. The inner flange is not cut yet to height. I will do that once all sides are drilled. What 's important here is to leave the cleco holes high enoug so that you can cut back the flange to 3/4" from the bending point and still have enough edge distance.
As the side baffles are also still a bit on the high side, it made the measuring on the position from the outside a bit more difficult. Overall I'm happy with the result.

One of the major issues I encountered is that with the current measured height - which is based on the minimum space required between plenum cover and cowling top - the diffusers no longer fit under the plenum cover (the opening between the front baffle stiffener and plenum cover as in the image above). 
Unfortunatly this means that I will have to modify the diffusers. Cut off a part of the top and lower it by almost half an inch.