Aieeeee! I just went through the exact problem that you’re having. About two months ago, my CPU fan died and killed my processor. The system has slowly been getting flaky ever since, but I thought it was just Windows Me being its corrupt little self. Wrong. When I tried to upgrade to Win2K Pro today, it got ugly. No matter what I did, the installer refused to recognize a hard drive to be able to install to.
Well, I figured out that my motherboard was to blame, so I went down and bought a new one. RAID technology, two IDE controllers and two ATA 100 controllers. I’m running an AMD Duron 950 processor. In short, my system is pretty similar to yours, now, and it still wouldn’t install (although it did get farther along).
Turns out that the Win2K installer doesn’t recognize ATA 100. Service pack 2 does (which can be downloaded through Digits’ link, above), but that doesn’t do much good when you’re trying to install. Leave it to Microsoft.
Well, I found a solution. I put my hard drives in a standard IDE configuration in the standard IDE primary controller. I ignored the ATA 100 controllers completely. Then I installed Win2K onto the system just fine. Once installed, I was able to install the ATA 100 drivers from the motherboard’s install CD. I then installed the rest of my hardware drivers (what few Win2K didn’t have already), followed by running Service Pack 2.
When all of that was done, I shut down the computer, turned both drives to masters, and moved them to the ATA 100 controller slots. My configuration is as follows:
Primary IDE – Empty
Secondary IDE – CD Rom and CD burner
Primary ATA 100 – Boot disk
Secondary ATA 100 – Second HDD
Note that I’m not running RAID, since my drives are different sizes and already contained data that I don’t care to part with just yet. But your process should be pretty much the same. Don’t forget that you also have to change your BIOS settings around each time you change the configuration. If your board is an ASUS, your boot order BIOS settings are going to be less than obvious. You won’t have any IDE hard drives listed in the boot order, when it comes time to set up for ATA 100. Instead, you’ll have to change the INT18 Device (Network) to SCSI/Onboard ATA Boot Defice and move it up to the top option. Mine goes SCSI/Onbard ATA, Floppy, CD-ROM, none.
In the same way, your POST won’t find any hard drives. They will be located after the POST by the ATA/RAID utility when it runs.
Anyway, 2000 Professional is running like a champ now, in ATA 100 mode. Oh, and one other thing: I stayed with FAT32. In fact, my computer guru buddies have all told me to stay with it. Since you’re building this machine just for graphics, your best solution may be different. But I wanted to pass the info along. FAT32 is faster than NT, for one thing.
Hope that solves your problem! It only took 10 hours today to solve it here, along with more cussing and swearing than I normally do in a year. 
Oh, and ZuZu: You can expect to be hearing from me soon for another permanent serial number. My office computer will follow pretty quick, too (WinMe is dying on it, fast).
