Just as a general aside for anyone who needs to know or is having the same problems themselves.

What I sent Canon at 11am 12/2/09:

Dear Canon support,

I’ve been having the same issue with my 5D Mark II for a while now. It does not focus well when using the peripheral focal points. At first, it didn’t focus well at all, even with micro adjustments, so I sent it in for repair. It came back still not focusing correctly, so I requested another repair. I then tried the micro adjusts on the center point and they worked, so I canceled that repair request. The I used the peripheral points again and the micro adjusts just don’t work, so I asked for another repair. It was right in the middle of my busy season though, and I never had time to send it off.
Reading the manual, I noted that the peripheral points aren’t as good as the center one, but the camera should still be able to focus! Thinking I could cope with using just the center point and cropping, I kept the camera yet again. Well, I can’t cope. I need to be able to change focal points. The included images are straight out of the camera, shot last night, only cropped a little to better fit in email. You’ll see that the first one is nice ad sharp in the middle, but the second one is horribly out of focus and soft when shot with the far right point.

This has been a 6 month long process. It’s been eating time and stressing me out. I need a camera that works the way I want it to (ie: a camera which can focus using the peripheral points!). I have considerable Canon brand loyalty due to use for over six years. Hell, I wrote an article for Canon: usa.canon.com/dlc/controller?act=GetArticleAct&articl…

A quick google search brings up a mountain of people who are having these same issues:
kareldonk.com/karel/2009/02/09/canon-eos-5d-mark-ii-not-w…
www.raoulpop.com/2009/02/27/canon-5d-mark-ii-soft-focus-d…
blog.planet5d.com/2009/06/canon-eos-5d-mark-ii-and-focus-…
fakechuckwestfall.wordpress.com/2009/03/09/eos-5d-mark-ii…

I don’t WANT to switch systems, but if I can’t get a camera that works, I will have to.

Where do I go from here?

Just now (8:30pm on 12/3/09) I got this:

Dear Heather Lickliter:

Thank you for contacting Canon product support. We value you as a Canon customer and appreciate the opportunity to assist you. We are very sorry to hear that you have trouble focusing when you use the peripheral focus points on your EOS 5D Mark II.

Regrettably, we cannot accept attachments at this email address. From what you have described, there is an issue with your camera that will require repair.

I cannot really say much about non-Canon websites, but if someone has an issue with their camera they should contact us. Your camera is not working as it should. I am sure that the service center can get the
camera operating properly.
We would like to send you a prepaid and insured shipping label so that
you can send the camera in to us free of charge.

I’m sending it back… again. I will have to spend another three hours resetting my settings and recalibrating my damn lenses when it gets back. I don’t anticipate it working when it gets back again, which will mean another round of pissed off letters and second guessing myself and thinking about a switch to Nikon. We’ll see.

I did play with a d700 and I purposefully didn’t use any of the center points. Oh, and hey.. all my shots were in focus! I think the things that impressed me the most were:
1. All the buttons! There’s a button for WB, there’s a button for ISO, there’s a switch to change the metering modes.. etc. I didn’t have to go through the damn menus looking for it.
2. The tracking. I switched it to continuous focus and half pressed the shutter while a friend ran around. I kept the point over her as she ran and the thing tracked her, keeping her in focus the whole time. I mean, holy crap, it was like something out of a movie.
3. Spot metering. The spot metering meters over the focal point you’re using, not like Canon where it meters the middle of the screen no matter what point you’s on.

What I didn’t like:
1. Canon cameras are just… prettier. Nikons look like they’re designed for old men.
2. No 1.2 glass.
3. The Nikon commercials with Ashton asshole make me want to poke myself in the eye.

All told, I really did like it a lot. 40 minutes in the cold isn’t really enough to base a switch on, but I didn’t run into any deal breakers. Another Nikon person says she gets 80% of s kid on a swing in focus. I know no Canon model can ever come close to that at all.