Now I understand what you're trying to do. First, I'd recommend leaving GRUB on your Windows drive, now that it's there and both Windows and Ubuntu are working. If you want to add another Linux distro, you can use the GRUB installation on your Windows drive to boot that distribution -- all you have to do is add another entry to your GRUB menu.lst file that identifies the new Linux distribution and its boot files. But before you start changing menu.lst, please make a back-up copy of it, and you might also want to keep your rescue CD ready in case something goes wrong and you have to go back to your original menu.lst.
If you decide to take your slave drive out of the computer, the GRUB install on your Windows drive will still let you boot Windows with no problem. It won't "notice" the missing drive unless you attempt to boot one of the missing systems, in which case GRUB will just return an error message saying it can't find the selected system.
As for your goal of having your second drive be bootable as a master -- that's where the problem that started the entire conversation lies, right? I'm still not certain what the situation is there. Even on your Windows drive, I think you'll find that GRUB is installed in a directory named /boot.
So, when you select Ubuntu from your start-up GRUB menu, it's going and loading GRUB from your slave drive, and giving you options that include your Ubuntu system and also Windows, right?
But, I guess, since your dual-boot system is working using the GRUB that installed itself onto your Windows drive, discussion of how to configure your second drive as a stand-alone master that can be taken and put into another computer if desired is probably wandering outside the scope of this "dual-boot" article. And into the scope of a GRUB-only discussion. (I happen to be writing an article on GRUB2 as we speak, by coincidence!)
So, does knowing you can put additional Linux distributions on your second drive and boot them from your primary drive GRUB installation meet your immediate need? By the way -- you'll have to be careful if you try to do this. The new Linux distribution could easily disable one of your existing systems. Ideally, you'll be doing this with all of your important Windows files safely backed up to another system!