I fitted a MFD2 DVD into my 05 GTI a few weeks ago, the friend who helped me (who works for company that deals with engine management fault codes for different garages) thought that the VAGcom might need to be told that the NAV unit was installed.
As it turns out it seemed to work fine except that I have difficulty playing audio CDs, they just stop or most of the time the unit thinks An incorrect DVD is inserted.
I am not sure if this is down to a faulty unit or some VAGcom issue (is this why they are on ebay)
I did consider sending it back, but decided it was too much hassle as I wanted to leave the NAV DVD in all the time anyway and use my ipod.
I installed a ribbon cable (half of an IDE cable) into the AUX connector so I could connect the ipod, and connected to the audio line in pins.

Also the instructions that i used and printed out ended up at the local VW dealer as they very interested too see how the swap was done (they had never done one)