I wonder if the neutral switch in the gearbox is getting a bit old? I'm thinking that if it's a bit dodgy, the ECU will think you're in neutral and won't let the turbo spool up too much, but you put your foot on the gas and release the clutch so the injectors do the full squirt, resulting in black smoke and a slight hesitance because there's not enough air ... have you checked the turbo is all ok? I'd assume so because lower gears seem ok (or you would have mentioned them), but anyway here's the checklist:
1) Remove the hose from the baffles or from the hard pipe going to the intercooler and wipe your finger inside the hose, then look at your finger under a bright light. Glitter is bad, it's a sign of a worn turbo.
2) Remove the hose off the front of the turbo and check the shaft for wobble (sideways movement) and smoothness of rotation. It may resist turning a tiny bit, that's normal, but it should be smooth.
3) Check the turbo's connection to the exhaust manifold, looking for black soot. If you see any, you may be leaking exhaust = losing pressure.
I suppose there might be an issue with EGR getting a little too excited, but it's unusual that it only does it in that final gear change, so I'd suspect the NPS first.
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