Hey kcfoxie
Your previous post lists a 2003 bug so I assumed you were coming from an ALH position. BTW, did you go 5 or 6 speed on your swap? Didnt know you had an 06. I have an 06 bug with DSG too and yeah, I know it's a PD and I know too that the ALH went out in 03. The 06 I have is a nice, nice car. Just bought it last July with only 6300 miles on the clock. It was just a baby and now I have it broke in for the most part. First thing i did was to inspect the cam since this car never saw a freeway in its 5 year proir to me owning it. I did know that the BRM was more susceptible on the cam issue. Seems that franko6 has a cam bearing mod that might just save the cam on both the BRM and BEW. Have you looked into that? Looks intriguing.
The 01M trans is indeed a mileage penalty piece of junk. I still have one bug left with the 01M. It's an 03 GL. I'd swap in a six speed if only my daughter could run a stick. So far I have converted my jetta and golf from 01m to the 6 speed and it has just made the cars a pleasure to drive. The best part was the mileage increase 42 mpg before and 50 after. Just converted my latest bug from 5 to 6 speed. 2375 rpm at 80

...now if only I could get better mileage out of my BEW. I average about 43-44 on the freeway which is about 4 mpg better then when I first got the car.
With that said, has the OP checked actual engine temp after warm up? How about EGR function and whether the flap that regulates intake is opening all the way? Malone was investigating this issue on the BEW as to economy that under some instances, that flap would not open all the way nor stay open as it should causing a lower efficiency. This he told me just recently and was also trying to find a way to monitor this with vag-com. Also what of timing as in torsion value? Would be worth to have someone check this. How about power on this car? Is it still normal? If not, turbo? Does the BEW use a snow screen as the ALH did? How about air filter?
I know some of these things are obvious, but this would be my road map.