Used to live in No. Va. (Oakton), but now live in Savannah. Wish I had found your car while I was up there! I have 2 560SLs (1988 with 102,000 and 1987 with 40,300--yep it's a cherry). Both cars exhibit the exact same "thunk" when the transmission is placed in drive--especially noticeable when backing out of the driveway and shifting to Drive. I've talked to others who also have the same complaint. Bottom line is: it's not a problem.
As for the blinker situation, that too is characteristic of the model. Surprised that you didn't mention hearing gas sloshing around in the tank when it is half-full and the radio and other noise makers are off. Both of mine do that as well. Hey, you'll get beyond these little nuisances and what you'll find is a helluva fine auto with lots of power and class.