I'd suggest that although the 1Ds MkII is still a useable camera, given the choice I'd go for the 5D MkIII, in fact I'd go for the 5D MkII.
16.7 MP and 12 bit processing with Digic II cannot compete with a 21MP and Digic IV let alone a new sensor and Digic V (if it's released).
Advances made over the early years of digital camera technology have been huge, now the advantages are tailing off, but I'm aware of Pro photographers who upgraded from the 1D MkIII to the 7D because in their opinion the 7D is a better camera. The 1Ds MkII is at least two generations old soon to be three (measured by image processor) You will be buying a second hand model, and most of these Pro cameras will have had a pro life, which means hard work how much life is in the shutter? Someone I know with a MkII had a shutter fail at 47K activations - below average but it can happen.
I'm not too sure what you think you'll be getting with a 50mm Zeiss lens that you won't get with the Canon, but I'll tell you what you'll lose - auto focus, and manual focus with a modern digital camera is not the easiest of things. If you want accurate focussing you will have to buy & fit a special glass screen (Eg-S for the 5D MkII) once it's fitted you won't want to be changing it for the standard one when you have an auto focus lens on.
If your photography has reached such a pinnacle of perfection that you really do need to squeeze the last scintilla of performance from a lens then it's reasonable to chase the best in equipment, but then why not just go buy a Hasleblad and a digi back? Or perhaps a Sinar & scan the film negatives.
If you are just an ordinary photographer like the rest of us it really isn't going to matter. Image professionals cannot tell the difference between a Haselblad & a G9 on large prints let alone between two different makes of 50mm primes.
No doubt someone on here will pipe up and tell you they can count the number of angels dancing on the head of a pin, but I will say forget the gear, there's more to photography that that, any of the Magnum photographers with a G11 will take a better photo than almost anyone else regardless of the camera they choose.