there is a intermittent flat spot at about 2000 to 2500 rpm and 3000 to 3500 rpm where in 5th gear or even sometimes in fourth, under acceleration it really labours
If pulling from a standstill, it will accelerate through all the gears without a problem
So does that equate to a flat spot between 2000 and 3500 rpm? Or you mean there are two adjacent flat spots?
Around 2500 rpm is the transition from n/a to forced feed, so fuelling is important. When you hammer her down and she picks up cleanly, that is because you will be getting the additional fuelling added for rapid accel calculated by the ecu based on MAP pressure and engine temp (accelerator pump on a carb analogy), and so will fill in the gap in fuelling. When you gently accelerate the ecu does not add any additional fuel than that demanded from the MAP sensor - so you will see a lag.
What boost are you seeing on your turbo at these times?
Can you check your fuel line pressure (is the reg ok, and fuel filter good)?
Have the injectors in your car ever been serviced?
Air inlet temp, MAP sensor and water temp sensors are important for the correct fuel calc in the ecu. These can easily be check as per the manual.
I may have gone off on a tangent, but would really need a little more info.