Heh, sounds like you've had a mess of a time. But FDisk (and I assume Partition Magic & MaxBlast also) works with whatever the BIOS tells it is installed. If either the BIOS or the drive aren't reporting it's geometry correctly, it'll never work correctly - that's why it's important to make sure you're square there. Since the problem only started after you tried to change the partition, it doesn't seem likely that the problem is there, but just to make me feel better check it anyway. I've only used MaxBlast on two systems, but it never failed to find (and identify) a drive, which is why I'm still concerned about this.
As long as that all looks correct, then the problem can only be in the partition table. If you have a WinME (or preferably Win98) boot floppy around, I'd recommend booting from that and running FDisk again. Try deleting a non-DOS partition, rather than a DOS primary or extended, and see if you have better luck. I suspect that Win2k would have to change the partition type from DOS to NT before reformatting for NTFS, though I don't know NT/2k well enough to say for sure. It doesn't explain why it's reporting the size incorrectly, but it would explain why it wouldn't delete. The delpart utility might also be worth a shot. It was part of the NT resource kit, but might have been included with 2k. If not, it's here
ftp://ftp.microsoft.com/bussys/winnt/winnt-public/reskit/nt31/i386/reskit.exe
If that still doesn't do it, give
fdisk d: /mbr
a shot. It's a reach (and I'm not sure /mbr actually works on an extended partition), but worth a try if there's no data to lose anyway. Win2k might cop an attitude about that when you reboot, but it should convert the drive again, and hopefully correctly. With any luck, it won't assume that it's supposed to be a bootable partition.
As for fixing the dual-boot thing, I can't help much, but I'm glad you mentioned it, it does present another (remote) possibility. I did read up on Win2k's approach to dual boot, but I'm afraid the bulk of it went in one eye and out the other. Win2k, if I recall, doesn't use a traditional master boot record, and the partition table of the primary partition (your C: drive) isn't "normal". Or rather, the way it's handled is a departure from DOS/Win98. At any rate, it's from your c: drive that it's getting the idea that you still have a dual-boot system, and the fix for it is different than earlier versions. I know there is a procedure to revert to a single boot, but you'll need to find it elsewhere. Win2k's help maybe? Heh, talk about reaching... At any rate, I doubt it's causing problems with your D: drive, but booting from the WinME or 98 disk will insure that it can't. I know that there was a lot of work put into recovering from problems in Win2k, and if it's trying to "fix" your "broken" other boot partition (without realizing that it isn't supposed to have an OS anymore), it's possible that it could give you headaches. That's just guesswork though, and I'll stress again that I don't know 2k that well, but if nothing to this point has fixed it, it's worth looking into. If you get it straightened out booting from a floppy and it gets screwed up again later, the guess is probably accurate and Win2k is "fixing" things for you. You'd need to get the dual boot straightened out first, then fix the d: drive again, then let Win2k convert it.
If
none of this seems to help, it's time to yank the c: drive and set the d: drive up as solo/master. Try installing Win2k on it, and see what happens. If absolutely none of this helps at all, and this doesn't work either, I hope your warranty hasn't expired. I'd have to chalk it up to hardware failure (as unlikely as it seems).