Does it shake when it's in neutral?, in all gears?, at certain revs? can you feather the accelerator to get rid of the shake? How's your clutch, does it slip if you get your revs/gears wrong? I had/may still have some heavy juddering after my remap. I've now had the inner CV joints and clutch replaced as that was slipping, hopefully it's cure my juddering, but I've not been on long enough journeys to know for sure. It was intermittent anyway, would do it for 20 mins or so then go away and was only on motrways. Alfatune told me it was the ECU sensing clutch slip therefore cutting power, therefore juddering.
It's also been suggested to me that swirl flaps could cause it, I've no idea what effect swirl flaps have, but it might be worth putting some soapy water on the flaps to see if you've any leaks. People have also suggested loose or split turbo hose.
If it's doing it constantly, I'd get straight to a Specialist, thy should be able to diagnose it.
GT 3.2 V6 - Q2, KONI FSD & EIBACH PROKIT, GTA REMAP, MICHELLIN PS3's, BMC CDA
159 SW 2.4JTDM TI - ALFATUNED, WIZARD BACK BOXES, KW V3 COILOVERS, NOKIAN WR A3/MICHELLIN PS3, PCA DYNAMICS ALIGNMENT.