Yeah it doesn't really occur until Ive been driving for 15 minutes or so. That lead me to initially think that it was a result of the CV joints needing to be re greased since that would give them sufficient time to heat up.
Interesting development though. I was giving everything a good look last night and found about 3 inches of water in the battery compartment so thats exciting as well, since about an hour after I noticed the shudder the SRS light came on with a passenger restraint malf. I am guessing the two things are unrelated since I can't really think of anything electrical that would cause this vibration.
2001 Jetta VR6