I've been reading about tranny/engine adapters for various Mercedes diesel engines that will allow one to accomodate various manual trannies. These guys have some wild stuff. This one is for the 617, I'm guessing the 616 perhaps has a different bolt pattern but I don't know. I do get that you'd have to be pretty damned devoted to the 240D to go this route, that is if it works.
OM617 to BMW 6 Speed 37DZ Adapter Kit
One issue I think I'm seeing, the models that sport this tranny are not common in US boneyards. They say the US model that has it is the E87 120d.
I found one on eBay for $1300. You can get a manual tranny for a lot less at a Pick n Pull.