So it WAS what Greg said above, unfortunately two of the flaps in my inlet manifold had given way. I had to replace the entire manifold, and because I sourced a brand new one it was not cheap unfortunately. Also, the GT TDI has a very particular manifold that is only found on two cars of that year I think.
The old manifold was completely clogged up inside too, the mechanic asked if I had a heavy foot, and I said maybe, and he then said that it must have been the previous owner that didn't give it enough boot to flush it out.
Some pics:
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