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I'm not going to read all 66 replies, so sorry if I am repeating someone else's advice, but a few things occurr to me.
1. Just how sturdy is your tripod and just how solid is your head? If you are using a cheap tripod, like you'd get at Walmart, the vibrations from the countdown timer will create some camera shake, as will mirror slap. That's why Canon's test "tripods" are massive chunks of concrete with threaded studs sticking out of the top. How steady is the rest of the shooting platform? Doesn't do much good to use a tripod if the floor is vibrating.
2. Do you get sharper photos with another lens?
3. How do you clean your lenses?
4. How long have you had that lens and do you use it a lot? Did it used to be sharp?
5. You might do better with automatic focusing. Cameras designed for automatic focusing tend to have focusing adjustments that are more extreme than cameras that are designed to be focused manually. A small adjustment to the focus on a lens for an automatic focusing camera tends to have more effect than the adjustments you make to lenses for manual cameras. This makes them harder to focus precisely in manual mode.
6. Your lens has a mnimum focusing distance and trying to alter that with a filter isn't going to work very well. Throw away the close-up filter and get an extension tube or a macro lens.
7. Do you wear glasses? Do you wear them when you shoot? A diopter adjustment does not turn your viewfinder into a prescription lens. It might look sharp to you and still be off.
8. Every SLR lens has a sharpest aperture. It will usually be f/8 or f/11, but occasionally it is f/16. Try f/11.
9. All the previous stuff said, your camera just may be in need of recalibration.