OK- finally repeated the test the RIGHT way this time. Warmed up the bike and did the 6th gear 30mph to 10 seconds full throttle test with the side cover on. Bike got to 46mph with the cover on. Repeated the test on the same stretch of road with the air box cover off and it did just a little better. Speed got up to 49mph this time and the bike did feel just a little better going through the gears. Still very low on power though and top speed was still only about 53mph.
What's next and thanks again!