Mystery horsepower loss - Can you solve it?

I have a turbocharged '99 Mustang with a built motor. It has Stage 3 TEA heads, a Typhoon intake, forged rotating assembly with 8.8:1 CR, and a custom turbo grind cam that is roughly .550" lift, 225 duration, 116 LSA. The motor is freshly rebuilt. The ignition coils and fuel system are aftermarket, and the injectors are 60-lb.

The turbo is a 76-mm from Turbonetics, and has been checked carefully. The hot-side piping is tubular and coated. It has been carefully checked for leaks. The downpipe is 3" and splits into 2x 3" at the tranny. The intercooler is a decent-sized air-to-air unit. The computer is stock.

Problem: We have been unable to get this car to produce more than about 475 RWHP, and can not get boost to go higher than 12 psi, even when blocking off the wastegate. Here are the symptoms and things we have done:
1) Backpressure is unusually high. We are seeing a 3:1 backpressure to manifold pressure ratio. We increased the turbine housing from a .83 A/R to a .96, but the back pressure remained the same. We made a dump downpipe to eliminate the exhaust, but it had no effect. Timing is in the 16 - 18 degree range at WOT. A/F is around 12:1
2) The turbo does not fully spool until 4,000 RPM. The engine seems to free-rev fine, and is responsive, but the turbo is way lazy.

Potential Causes:
1) Retarded timing: We have checked the timing, and it matches the computer at the engine.
2) Camshafts ground wrong: We have checked the cam specs with a degree wheel and they seem to be ground correctly.
3) High resistence intake plumbing: The boost at the turbo is within 1psi of the intake

We are at a loss to what is causing the problem with this setup. This system should be capable of well over 600 RWHP and more than 20 psi if we wanted to go there. What is causing the problem??? Think you know the answer? We would love to hear more ideas...

Back pressure measured at turbine inlet

Boost pressure measured at compressor outlet and intake manifold. Both are within 1psi of each other.

The intercooler is a decent-sized air-to-air. Already checked for the rag-in-the-intercooler possibility, plus the pressure difference between turbo and intake manifold is 1 psi.

Boost profile is that 1psi comes in at around 3000 and 12psi at 4000, and then roughly flat form there. In general, it feels laggy, and wasn't any better with the smaller .83 A/R turbine housing.

Not sure on the blow-off valve. I'll check that. A leaking BOV would be bad, so I'll check.

The Typhoon intake was put on the car AFTER testing with the stock intake. The stock intake had problems with the water neck, and was leaking. I tried a second stocker and it cracked from boost at the molding plug. The Typhoon is brand new and has been fine. It was torn down, carefully inspected, port matched with the heads, and reassembled with sealant at the gaskets. I am pretty sure it is not leaking.

12:1 is for low boost. As manifold pressure rises above 10 psi, it starts heading towards 11:1

The transmission is a manual.

The coils are the Granatelli hot coils.

By "low-boost A/F" I mean the air/fufel ratio at low boost conditions, which I consider to be anything under 10psi.

I am not really sure who made the hot side. I bought the car years ago, and it already had the headers. They look like an older kit, but I can't identify it. It is 1&5/8" tubing, and seems fine for the horsepower level of this car. It doesn't have any sharp bends or other unusual flow-limiting geometry. Keep in mind, I am measuring backpressure at the turbo, so the headers aren't the problem.

I haven't specifically checked the intercooler for leaks, but I can look for a crack somewhere. Not sure who made the intercooler, but it looks fine, decent sized bar-N-plate type.

I used both a regular plastic-only, and a second stock intake with the AL water crossover, and had problems with both. Both were used, but in good condition. I have heard about many boosted cars having problems with these, and if I go more than 14psi I don't want problems, so I switched to the Typhoon. There is nothing wrong with the Typhoon intake that I can see. I don't want to switch to a Edelbrock and then have to change fuel rails, intake plumbing, throttle body, and all that stuff... especially when the Typhoon seems fine.

We ran the car with the compressor disconnected from the intake tubing, and we registered 13 psi backpressure. This is 20+ psi less than when it was connected and making 12psi boost. I was hoping the backpressure would be even lower with the compressor disconnected, but I am unsure if that is a decent result or not. Has anyone ever run that test before?

Next, we are going to run an intake plumbing leak test.

I did pressure test everything yesterday, I could only find 2 small leaks, 1 at the IAT sensor and I put some permatex grey around it and there is a cap on the IAC valve that almost seems like a relief valve that has a very small leak...nothing that I could see that would cause a large boost loss really - the intercooler, BOV, intake, were all leak free.

We are going to do a coil test with a spark gap, and also check the voltage at the coils when under load. They haven't been missfiring though.

Any other ideas?