http://support.microsoft.com/default.aspx?scid=kb;en-us;160963
Ok, I'll answer my own question. I used this article to help me figure out how to skip the chkdsk on reboot. What causes the chkdsk to run at boot time is a setting in the registry that causes program called autochk to run. That setting gets there if the disk was brought down inappropriately. So, change the registry setting and then it will reboot without running chkdsk.
This article discusses a program called chkntfs that will allow you to change the registry setting. But part of my problem was that chkntfs won't modify the registry setting if the drive isn't available. And ofcourse it wasn't since I couldn't boot my machine with that drive hooked up. So I unhooked that drive, booted the machine, and modified the registry setting by hand.
I just set it to "autocheck autochk *" (w/o quotes). Ofcourse you must be careful if you set anything in the registry by hand. This article also makes note of that.