I'm having the exact same problem as you in my 55 plate GT 1.9 JTDM. Started last November, and equally only becomes an issue on long runs (which I do twice a week). I notice it happens under load in a high gear - throttle balanced - so if I start to go up an incline and don't immediately change down (ie an incline that would normally be fine in 5th or 6th). I have also replaced the MAP, and the VNT solenoid too. I normally drive alone on the long runs - but recently had the family with me and it would go into limp mode constantly, whereas alone I can sometimes coax 40 miles out of her without having to do a stop/start. So it would seem under load that it overboost more. Usually if I drive with plenty of revs, and avoid 6th gear, I can stay out of limp mode the most. When it's not in limp mode, the car has loads of acceleration (have had the EGR ecu-deleted) - so it would seem the turbo is in reasonable condition (the car is on 120K miles and has a full service history).
I am due a service now, plus the thermostat would seem to need replacing - having always been sat very close to 90, it now sits at 70 most of the time. So, I'm hoping with the new air filter, a new thermostat and an ecu reset, it might improve. Otherwise I'm planning to try a Mr Muscle treatment on the turbo vanes to see if that might cure it. It's a real shame, as otherwise the car runs really well and until recently almost always averaged 50mpg brim to brim. The last 50K miles/3 years have involved twice weekly 100-140 mile drives - maybe it's been sat in 6th gear too much?
Anyway, good luck with yours - there'll be plenty of suggestions no doubt - seems one of the most common issues.