[JustOne]

Looking at your dyno graph I am a little surprised that the motor made peak power at 5600rpm, and was about the same from 5200 to 6000 rpm. These are results I would expect from a smaller cam. What horsepower and operating range did your builder tell you this motor should run in? I know that going from 10:1 to 13:1 on a dyno is usually worth 50-75 hp, and with a 13:1 motor and the BlueThunder set up I would expect you to be in the 600-675 fly wheel HP range. I would check to make sure the cam is degreed in properly, then recheck timing, and maybe have the heads flowed if you haven't already.
On the chassis dyno a power drop of 100 hp seems to be common, with some as low as 75. I think the mufflers you are useing are very good and you shouldn't get more than a 15 hp loss if any running open headers.
For peace of mind either buy or have a forum member run your head data with flow numbers, cam, and induction through desktop dyno and see what you come up with. If you decide to buy the software I think it is only $50.