Part of your problem is that your intake runners are too long for the power band your cam supports. Remember, long runners are geared to more torque at the lower end. 6500 rpms is way out of range for a Cobra intake. You should have a shorter runners. A box intake would be easy since you already have the lower intake, but a Trick Flow (The one that is comparable to the 351 intake) intake might do a better job.
The people doing the dyno tests clearly don't understand what torque and horsepower are so I would take it elsewhere. Torque is measured, horsepower is calculated. If the dyno can't measure torque, you can't calculate horsepower.
Regardless of what the actual numbers are, your peak horsepower is probably at the correct place. 322 RWHP isn't shabby for what you have, btw. You're putting out 380+ HP at the flywheel.
I wouldn't worry about your exhaust. That's not your problem at this point.
------------------
351W 89 Mustang GT Convertible