Just let it run down to a point where it stops by itself to finish the calibration. What it still doesn't know is how far it can go, and the only thing to make that happen is to let it drain over the normal course of use.
Are you having any problems keeping it charged and it plays out at a bad time? I run min a good 12 hours of fairly heavy use, markets, news, downloads and it usually get down to the point of I have less than 5% remaining then I get home and its going on 13 to 16, use it for mail and TV Guide and after about 18 hours I plug it in by my night stand and take it off charge when my alarm goes off.