The shots from your 20D+400/5.6L appear sharper and with finer detail. Not knowing how big the crop were it's not easy to make direct comparison. Were you shooting RAW on the 20D then? Pixels size in a DC is not everything ...
Post processing can make a 'night and day' difference to your final output too. The U4R result is quite impressive IMHO.
Best & Good Shooting!