How much boost and timing? who in MI tuned it, toss the C&L, run a 03-04 cobra MAF+ MAFIA or SCT meter. your power sounds about right, Most of the MI "tooners" will not put enough timing on these cars, I'm guessing they gave you there "Safe Tune" w 17-19 deg. AF in the high 10's low 11's
So many factor's here, besides the obvious of number's being number's and dyno's being test and tune tool's, how does the car feel driving it. Who built the engine? with 04 cobra internals you are lower compression and with 12 psi and low or average timing the power sounds about right, if the blower has a good port, you can increase boost with a lower pulley and add some timing to get to your 500rw goal. if you open up the inlet with a dragon TB/plenum you might pick up 1psi. if you have headers and no cats, or belt slip it might explain why you only see 12psi.
You also mentioned you pegged the MAF, at what RPM? maybe you didnt spin the car to peak power before it pegged. just some ideas. Good luck