I think I am beginning to understand some of the speed difference. It started with a bad assumption.
There was a previous thread on this forum that suggested moving from a 55 pitch to a 54 pitch prop would require readjusting the power tables by 100 RPM. Last summer with the 55 pitch prop I made all of my measurements at 2000 RPM trying to base line the POH max cruise tables best I could. The cruise tables are based on 2100 RPM with adjustments for altitude using a climb prop. So when I started to make measurements post cowl flap and prop change I made my runs at 2100 RPM where I started to see the 5 MPH speed difference. I don't think there is a 100 RPM difference for same power settings between the 54 and 55 pitch prop.
Here is a screen shot of my baseline measurements in June of 2010 just after getting the airplane. No modifications. This screen shot was taken as it was delivered from the factory in April of 2010.
Now here is a screen shot from taken today under similar conditions. The difference now is the CC has the new cowl flaps, partial closure of the oil cooler fins, lower cowl extension I have described in other posts and the new 54 pitch prop. Disregard fuel flow reading differences as I adjusted the "K" factor over the winter. Fuel flow in the picture below is correct. Fuel flow from last year was reading high.
There was a 4 dF difference in OAT between the two runs (last year versus today) but note the difference in CHT's. Running 3 mph faster today while running at 2,000 RPM.
So putting it all together I now have a Carbon Cub that is running a little faster and significantly cooler that it was when it was delivered in April of 2010 with all of the cooling modifications. I am happy with the result.