No worries, you did it properly.
Open HijackThis and click on the "Scan without saving a log" button. Look for these two entries and place checkmarks next to them:
O13 - Gopher Prefix:
O15 - Trusted Zone: http://*.download.windowsupdatecom
Close all other windows/programs and click on Fix Checked. That aside, your HJT log looks pretty clean. It looks like the scans cleared up your infections pretty well. Are you experiencing any problems?