I don't think that it's the lens. I was having an issue where if the lens was set wider than about 50mm I would get the error99. I was also having issues with the shutter release button not taking the picture when pressed, sometimes it would fire about 2 seconds after being held down. I tried taking out the battery, taking off the lens and removing the CF card for twenty minutes. I even cleaned the lens contacts. Amazingly I was able to fire a couple of shots at 17mm and then the error99 came back.
So I took the battery out and I also took out the little battery that stores the time and date. I had to reset the time and date but now my camera works like new. No error99 so far after testing with a couple of dozen pictures at every different focal length and it fires. I noticed before I took the little battery out that switching from Raw to large fine made a little bit of difference and it would have probably limped along. But I like shooting Raw, it's part of my workflow.
Hope this helps someone else. I was about to take my camera to Canon and would have probably spent a couple hundred dollars easily.