I've had this problem since fitting a "reconditioned" gearbox along with a new clutch to my Mk5.
I Fitted a new crank seal and input shaft bearing (Genuine Ford) at the same time as the gearbox, so in theory the rear crank oil seal output bearing and clutch should have been OK!
The problem doesn't exist when the engine is cold but worsens when up to normal temperature and is highlighted even more when loaded.
Keeping the revs a little higher than would normally be required when pulling away or reversing makes the problem dissapear.
So I investigated all the usual recommendations engine/gearbox mountings, propshaft alignment & bearings, rear diff bearings all to no avail.
So I removed the gearbox (for the 4th time, don't ask) and the clutch, and it could be seen that the clutch plate hadn't been running perfectly true by the marks on the flywheel, further investigation revealed the input shaft on the gearbox is very slightly worn at the point where it sits inside the rear crankshaft output bearing.
I'd retained the old bearing (which wasn't at all worn but as I'd bought a replacement I had fitted the new one), and discovered after taking some accurate measurements I could install both bearings into the crankshaft and install the gearbox OK.
This hasn't entirely celared the judder but has improved things until I can get "another" replacement gearbox this time without a worn input shaft.