Tuning problems

I have a huge problem that I can't seem to figure out. I have a 2000 trans am with stage 2 heads, long tube headers, comp cam, ls6 intake, bbk throttle body, undrive pulley, slp intake and maf, msd wires and of course free mods. My car is not running near as good as it should and is only pulling 365 hp to the wheels. I have had it on the dyno twice now to do tuning but it drops the rpm feed under load on every pass. We have checked everything and cannot find the problem. I would greatly appreciate some help or ideas. The package we installed should be pulling 400 hp to the wheels and seems like it will with tuning but we are unable to any. Thanks

Which dyno ... Dynojet or Mustang? A Mustang will read 10-20% lower than a DJ will.

Whose stage 2 heads? Flow numbers?
Which brand headers and the balance of the exhaust system details are needed.
What are the cam specs?
BBK TB is a POS
Anything other than a stock MAF is suspect. Many documented problems with Granatelli and other's MAF

Who did the tune? Reputable?

My '98 TA with LS6 intake (!EGR), Fuestel ported heads, stock cubes, FLP LTs through a Borla and cats, Comp 220/.558/114, stock pulleys and a custom tune by LG Motorsports on a Dynojet put down 380/380 at the wheels.