I suck at focussing my 5D

Some lens are just worse than others thats my experience anyways.......
I have found shoot lots and you get a feel after awhile and know what the cameras quirks are so you stop doing the things that cause this action cause i rarely have images do this to me anymore, at the start of the canon thing for me OMG yea i was frustrated!

Flip the lens into manual focus mode and play with that feature vs af see what the diff is...... or find that point where you know what lens is bad where.
I hope this makes sense this is what i did if i found it was just way too much to deal with i sold the lens and got something else in which everything (Lens wise) i have now is fine no issues..

If you focused right on his eye with 1 single focus point, it should fall on his eye, so I would say it needs calibration because it's "back focusing" as they like to say. I would totally peep that, his sideburn is hella sharp but his eye is not. I calibrated my 50 to +3 on my nikon, it was sharp as a tack on my D80, and not so much on my new camera, the +3 fixed it so now its super sharp.

Edit, I just saw you used MF? Try with AF when you test it and make sure its locking on good. I do a very LOW FI focus test with my camera. I sit down, and watch my daughter play and when she holds still I ask her to look up, if her head doesn't move I take a shot and if I know my hand didn't move and she didn't move I look and then adjust my calibration and test it a bunch. It would be easier to test with my husband as he doesn't move but he's not as easily entertained I also always keep my SS above 200 when I test and I test at a shallow DOF so its easier to tell what is and isn't in focus and by how much. I find eyes are really good to test on and more "real world" for me, and I can easily see if focus fell on the hairline or back on the ears etc (doesn't help as much for front focusing but I hack it out).

seems like back focusing to me. Next time just focus on the tip of the nose and you should get it lol. My pictures are front focusing which is much more of a pain to deal with. If you have micro adjust then just use it

Okay, I think some people didn't read the OP's post closely enough. He manually focused the lens. Now, the question is: did you focus and try to get the eye as clear as possible, or did you focus until the little red focus square lit up under his eye? If you did the latter, than I believe that's your problem. The focus point wasn't at a good area for contrast, as mentioned previously. Adjust your diopter for the clearest view, then trust your eyes. If you feel the need, use live view and zoom in. I agree that modern dSLR's aren't as easy to manually focus as older film cameras, but the 5dII is probably easier than most, what with its big viewfinder and all.

Hope this helps.