Guys,
Thanks for all of the assistance. As promised, I said I'd update the thread when I found a solution. It turned out to be the fuel pump. I fitted an aftermarket PWM pump which is a direct swap and has the fuel level sender incorporated. This pump is compatible with the 225bhp BAM engine so it should flow a decent amount of fuel.
My car was pulling back on boost and was very stuttery between 3000rpm and 4500rpm, it just didn't want to go at all and it was showing as running lean on VAG-COM. It was dropping requested boost and the wastegate duty cycle was very low. It was getting worse to the stage that the car was shuddering on full throttle and wouldn't go over 3500rpm in 4th gear. The boost fluctuations and forced closing of the throttle butterfly also caused my charge pipe to pancake pipe hose to pop out of its clamp.
I changed the pump today and the old one looked very dirty inside the fuel supply port. The return port was clean as a whistle so I assume that almost 8 years of fuel delivery was as much as the original pump could manage.
No bad thing but I've replaced the following items on the car in the last 2 weeks trying to get to the bottom of this:
MAF sensor
Coolant temperature sensor
Thermostat
Injector o-rings and manifold inserts
Turbo Intake Pipe (fitted a forge one)
Boost hoses (4-ply red silicone)
Fuel filter
Front (pre-cat) Lambda Sensor
Hopefully that lot will keep her ticking over nicely for a while. I've ordered a new charge pipe to pancake pipe boost hose, clamps and o-ring and I'll be fitting that tomorrow.
The car is now absolutely flying, I'm finally able to enjoy the benefits of APR Stage 2.
Will post some logs tomorrow to show the difference.