This could really be a can of worms. The following is just my extrapolation from previous experiences that do NOT include doing the type of installation you propose. What file system is the Windows 2000 disk / partition using? If FAT32, then NT4 isn't going to see the drive's partition properly, but it would still need to write to the MBR of the first drive (wouldn't it?). If the Win2K disk is formatted NTFS, then you'll have to be using an NT4 SP4 disc or later in order for NT4 to be able to see and read / write on the Win2K drive. Even if you manage to get the install done, you'll then have to do a FIXBOOT-style repair from the Win2K setup CD because more than the boot.ini needs to be changed. The MBR will have been overwritten with the NT4 version which won't, AFAIK, work for Win2K. One good thing would be that you could use Win2K's disk manager to prep the second drive for the NT4 install. That first partition on the NT4 drive could then be the theoretical maximum of 7.8 gigs for an NT4 boot partition, and the MFT for the partition would be in an optimal position because the drive would be pre-formatted NTFS instead of converted the way the NT4 self-formatting / conversion feature works during NT setup.
I'm a simple guy. I'd do it the simple way. I'd start over and install NT4 first, then install Win2K on the second drive. The last I looked, Microsoft advised against dual booting NT4 and Win2K right inside the same MSKB article that told you how to accomplish it. They always recommend installing old first, then newer. And I don't like to look for trouble.
Good luck! I hope you'll post what you do and how it turns out.
- Collin
