Hi David,
I tell you my experience with the 5D II: the first shots I made where just a bit out of focus, I thought my eyes where not working so good...
The truth was the camera had bad alignment of maybe the sensor or something else. I have made test shooting object like a keyboard, focusing on a precise letter on it and the camera gave me the letter out of focus of a bit. This was made with 3 lenses I own, 100 macro, 70-200 2.8, 90 tse, all on tripod, MLU and cable.
Next day I brought it to the shop and tested there with my mac and tripod another body, the new one was perfect. I was lucky the seller had still one body on sale!
Have a test with or without live view of a small object with a macro lens and you will find if there are sensor misalignment issues... thanks to canon quality control!
Good luck
Best regards
Roberto
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www.robertopastrovicchio.com