Hi Tim. I have had some problems too as i guess have many people. That is a good way if you have EOS Utility or similar program, you can view the images after they transfer over. I found i did quite a few test shots at about 5 sec eposure then zoomed in after to try and get good focus. I also found the focus ring to move after i had set it in MF on my 50mm f1.8 nifty.
I found with my lens, good focus was all the way anti clockwise (from looking through viewfinder) then back just a tad.
Apart from that i cant think of anything else, hopefully others will have ideas. Good luck