Ford Focus 1.6TDCI with pulsing revs

First of All
Hi Guys it has been a long while since I was last on here (when the german uni? stopped offering free access)
Now, as ever I need a little help.
I have a mk2.5 Ford Focus 1.6TDCI 109 (the french engine) the car is one of the few on a 08 plate (most are 58 onwards)
The car has always had a peculiarity in that on a run, when up to temperatu re it will have a period of loosing power for 2seconds before recovering, t his usually is accompanied with a puff of white smoke. When in this mode it will smoke steadily on the over run, or on tick over. Left alone this usua lly clears itself after 2-5mins and normal service is resumed. The smoke sm ells very dieselly.
Ive always put this down to a regen taking place.
Now the car has another issue where it seems suffering with a similar surgi ng/drop in power but pretty much all the time. If I run it in neutral at ab out 1700rpm, where the turbo starts to kick in I can hear a rythmic dull th ump then the revs drop slightly and the turbo whistle changes tone, before a second or so later everything goes back to normal. I have noticed this on a few occasions.
On this occasion There is a wee bit of smoke, but the engine was VERY cold and battery quite low so I dare say the glow plugs were not running at thei r optimum.
Any offers on what is going on here? EGR?
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