I've shooting Jewelry for a few years now. When I got my 5D original images where outstandingly sharp for the file size. I use 100mm macro, 50mm macro and 90mm ts-e for this kind of work. My cameras is always on a tripod and mirror lockup being used as well as self-timer.
Ever since I moved to 5D MKII things changed and My details are soft compare to those of the 5D original. I have tried everything from working a bit wider F/16 to focusing via Live view and no luck whatsoever.
The problem since to be worse while working this close range than when working normal distances.
Anyone would have and idea of the problem. I have read many forums and what I have pick up from them could be the lenses not performing well with 22 mp.
If you are using live view 10X and manually focusing focus should be good. Are you comparing 100% crops or the same amount of the subject? I am finding my 5DII sharper than my 5D? perhaps you are running into diffraction sooner maybe f9 and focus stacking would help.