Can I suggest going back to basics. Here are some thoughts in a random(ish) order.
- if you are using a long lens (i.e. 90mm), even at F32 and viewing 100%, the images will not be sharp front to back. A small zone, wherever focus has locked, will be in focus but it is unlikely to cover the front to back of your subject. As has been mentioned above, your camera will be making this worse due to diffraction.
- What tripod are you using? A flimsy tripod will move as the shutter is fired. You will never get a decent picture if that is the case.
- If you want critical focus, and as you are on a tripod, use a part of the item that has some decent contrast and then use live view focus. "Normal" focus can be out depending on the body and lens combination and if you are taking shots you need to be critically sharp at some point, you need to get the bit you want critically sharp to start with. Live view will do this whereas phase detect (the through the lens focusing) can cause problems and errors.
- Are you using flash or just ambient? Artistically a couple of flash heads are going to do more for the photo than achieving critical sharpness will ever do.
- If you shoot flash, the flash takes the photo, not the shutter. The shutter exposes for the ambient light. You can put your shutter at any value within reason and you will be fine.
- The 550D is an 18Mpix sensor. It needs decent lenses to be termed "critically sharp" IMHO.
Bottom line is that it's probably your technique at fault or your expectations are too high for what can be achieved with the setup you have. Just as an example, here is a 100% crop of what you can achieve
hand held with flash (focus was at the centre of this 100% cutout) at 70mm full frame lens equivalent (I've cropped as forum rules are 800 pixels max side).
and if you want to see what the depth of field is like at f9 (this is on a micro 4/3 camera - the 550D will have slightly shallower depth of field) see the full image here:
http://www.arad85.co.uk/hosted/talkp/P1000395-full.jpg