I recently decided to finally put Linux on all of my computers, not just a few. So I whiped out my desktop and put Gentoo on it.

Now I'm coming around to the fact that for a few things I do (Primarily gaming) I will need access to a small windows partition.

So... I have a bit of hard drive space set aside on my 2nd hard drive for windows... formatted in FAT32 so I can mess with it from my Linux boot, which will be the main. The problem is of course I was foolish in not installing it first, so now i'm having some little issues.

The main problem is currently that while trying to installed windows 2000 on the second hard drive, it demands space on the first hard drive for something it needs. I can only assume this is for a MBR(is it?). The problem is, I don't really have any leftover space. So i'm left with a few options.

1) I could slightly reduce the size of my swap partition, to free up some space for it.

2) I could simply remove the first hard drive, install it on the 2nd, then reconnect the first.

Does anyone know a best way to do this? Also, in the case of 1), would Grub be overriden? And in the case of 2), would the computer have any problem with their being an MBR on both disks? How would it act?

Any help will be appreciated.

Installing windows after the fact will cause problems, but it's not as bad as some folks make it out to be.
First, make a boot floppy or boot cd for the Linux installation. Windows WILL overwrite the MBR on the master disk. The only way you will have of booting Linux is from boot floppy/cd/install cd.
Second, install windows and suffer the indignity of having the MBR overwritten.
Third, when windows is installed, reboot (required by windows, not Linux) to be sure the installation was successful.
Fourth, put the boot floppy/cd in the appropriate drive, and reboot. Your Linux should boot up.
Fifth, re-install the bootloader (not the same as installing software, just re-install to the MBR. There are tons of posts in these forums to guide you).
Sixth, edit the bootloader config to add the windows installation. There are also instructions in these forums on what entries to make in the config file to convince windows that it's on the master disk when it's actually on the slave, and boot anyhow.
Those are the steps to follow. I leave it to you to dig out the gory details.
Your option 2 just adds unnecessary complication.
So far as I know, there is only one MBR (the one on the master disk). However, you can make partitions on the slave disk bootable, if the bootloader is written to the partition in question. Folks do it all the time with several Linux distros. One has the master bootloader written to the MBR, and the rest write their bootloaders to the partitions they're installed in.
Of course, it's necessary to edit the bootloader config file of the master to tell it where all the other bootable OSs are located.

The little bit of free diskspace Windows requires during installation is as far as I know some kind of ramdisk it generates to put temporary drivers for cd-rom-drives and similar stuff on. I think it needs only around four to eight megabyte for that and it's nothing with the MBR.

So what about the possibility of just removing the first harddrive, booting from CD to install windows on the second hard drive, and then when it's successfully installed, reconnecting the first hard drive?

I could just add the 2nd bootloader as a bootable option in GRUB? In the end that seems easier to me. I'm not confident in reinstalling the MBR and bootloader.