I don't know that you are throwing good money after bad money by sending it in. Heck, it's under warranty. When I sent in pictures, the CPS rep looked them over and made his opinion, then shared them with a group, who made an opinion. Without knowing the other's opinions, they all came back the exact same - something wrong. If you think something is wrong, send it in or exchange it.
Not sure where you are located, but I'll be glad to take a look at it with my lenses and give you my opinion.
I am in the middle of nowhere, Google labrador city. About 12 hours drive to the nearest city.
I read the article on focus adjustment the canon customer service agent sent. It doesn't go into great detail but does suggest that MFA may not be reliable on third party lenses. Right now the plan is to reset the camera back to factory just in case I have changed something that is causing the problems; concentrate on using the canon lenses and see if I can get any shots that really prove there is a problem. Twice now I've seen adjacent shots that were wildly different. The first time with the tamron and all were soft except one in the middle of a burst with MFA off that was very sharp and the second time while doing the focus test shots for canon where all were quite soft except for one that was completely out of focus. I need to carefully document this random error in pictures. As all lenses work on my T3i I do not think it is a lens malfunction issue.
If I can get it to work with my canon lenses then I will have to re-evaluate the situation. My opinion isn't cast in stone yet but I am coming to the conclusion there is something wrong inside the camera.
What would I use to clean the electrical body / lens contacts?