I believe the downshift thunk went away when I changed the front flex disc. I know the rear flex disc lasts a bit longer... but maybe it could be the rear? Maybe it should be inspected. How many miles do you have? Also maybe check the drivetrain mounts.... ie differential mounts, trans mounts.
I don't think that your fuel door vacuum is related to engine vacuum... it is operated by the vacuum pump, which is not related to the vacuum suppled by the engine (i believe?) which controls trans shifting.
2006 E350 w/ 155k miles (Daily Driver)
1993 300E 3.2L Sedan w/ close to about 300k miles
2003 E500 Brilliant Silver (Had 217k miles when totalled!)
1989 300E with 289,000 miles (had for <1 yr while in HI)
03 CLK 500 cabrio (Mom's)
2006 C230k (Dad's)
1999 S420 (Mom's/Dad's)
2000 C230k Sport sedans
2001 CLK320 Cabrio (Mom's)
1995 C280 My First Mercedes-Benz... (155k miles. EXCEPTIONAL AUTOMOBILE. Was Very hard to let go of!)