Your active Windows files are almost certainly on the Primary Master drive - usually the C drive. You can confirm this by simply unplugging the second drive. If I'm right, you can save disk space by deleting the Windows files from the second drive. I think it's most unlikely that this is causing the slow boot up. Try clicking Start - Run. Type in msconfig, then click OK. In the System Configuration window, click on the Services tab. Click to tick the "Hide All Microsoft Services", then Disable All. OK out of the System Configuration Utility. Restart the computer, ignore the warning about having used the System Configuration Utility. If the boot time is faster, incrementally re-enable the Services a few at a time STARTING WITH THE ANTIVIRUS, until you find the cause of the slow boot-up.