Many thanks for all the help and advice so far. I found some time the other day to go through some suggestions, I had a little success micro adjusting the lens just through trial and error, but over all I am still not too pleased. I have tried with EC .7, and mid range ISO as previously suggested but am finding noise and a lack of detail.
If you are finding some improvement with micro adjusting then you may need to the the lens/camera calibrated. The problem with micro adjusting a zoom lens is that it may require different micro adjust at different zoom settings. The only way to do that is to send it in to Canon and have them calibrate the lens/camera combo.
How long have you had the lens? If you are still in the return window then maybe swap it out for another one.