I think you may mean the actuator arm may be seized.
VGT's don't have wastegates.
I think it may be the EGR valve stuck open.
39k sounds a bit low for the year, so I can only guess the car is getting "local and light use" and probably hasn't had the gunk blasted out of it with long motorway runs.
It's a very common issue with common rail diesel engines as they've tried very hard to clean up their emissions.
Soot and oil vapour from the crankcase breather (which will feed into the air intake somewhere along it's route, again sent in there to burn to clean up emissions) get blown up to this valve, mix and cause a right mess, gumming the valve up like this
http://t3.gstatic.com/images?q=tbn:ANd9GcQNY6XHxisUwSYTfSwBm56-dZTtJcvjPimg4aDFXpnB10MJdabtY8fKXbWE
The OP seems to say the car runs ok up to a point, then when it's floored it stutters, loses power and lights the MIL, seems to point to the turbo being ok until something else happens.
When the car has an open throttle the egr valve should be firmly closed (it should only open on part throttle like a steady cruising speed and under certain conditions to lower combustion temps which lead to cleaner emissions, The sort of speed and load the valve should open, could or could not have something to do when emissions measurements are taken!! You make your own mind up
)
If the valve is sticking open and the pedal gets floored, it'll stuck in a load of exhaust gases which are full of Nitrogen Oxide instead of all the air it needs to burn the fuel it's just dumped in there.
The NOx won't allow the fuel to burn as well as air.
It's not good at allowing combustion, think back to fire training, take away either the fuel, heat or oxygen and the fire goes out (the fire triangle), well NOx takes away oxygen and heat.
NOx also cools the combustion that does take place, add both effect together and it'll lead to the hesitation, loss of power and in some cases the MIL lighting up, it's effectively choking it's self on exhaust gases.