OK, I finally "bit the bullet" and tried changing my disk partitions.
I used the Ranish partition editor, which I was very impressed with, thanks Ninho!
Well, after lots of agonising and head scratching, I'm now back as I was before!
It soon came back to me exactly why I had the drives partitioned as they were.
I converted the D: partition to a primary partition with no problem.
Unfortunately, when I rebooted I discovered that it was no longer drive D:!
It had become drive F:, and the old E: had become D:, and the old F: had become E:.
This is no good, because although I can redefine the drive letters using Windows 2000's disk manager, this does not change what DOS and Windows 98 sees.
The whole Windows 2000 system configuration depends on Windows 2000 being on the D: drive, and I certainly don't want the drive letters being different on the two operating systems!
No matter what I did, I couldn't resolve this.
If I disconnected the other two drives, the Windows 2000 partition became D: again.
However as soon as I reconnected the other SCSI (E:) drive, it became D: and shunted the Windows 2000 drive down to E:.
Even deleting the partition and reformatting the other SCSI drive didn't make any difference, it always became drive D:, whether it was a primary partition or a logical drive within an extended partition.
(Many hours I spent verifying and formatting drives yesterday!)
To add insult to injury, this didn't even do what it was supposed to do!
I had the system with just one physical disk connected, partitioned into C: and D: drives, both primary DOS partitions.
Windows 98 on C: and Windows 2000 on D:.
All worked fine, even though I couldn't leave it like that as I obviously need the other drives.
I then put the Windows 2003 NTLDR file into C:\ and rebooted to Windows 2000.
Exactly the same result as before -
"\WIN-NT\SYSTEM32\CONFIG\SYSTEM is missing or corrupt".
So the whole exercise was a complete waste of time!
The 2003 NTLDR still doesn't work on my system even if Windows 2000 is on a primary partition.
In fact the only way I could get the drive letters to be what I wanted again was to reformat D: as a logical drive within an extended partition, as it was before.
Then adding the other drives (also logical drives within extended partitions) didn't change the drive letters.
So, a large number of hours spent, terrified of losing my data, all for nothing!
Anyway, I am now back to normal, and haven't lost anything, apart from a day of my life.........
What I'm now considering is whether to try changing over the two OSs, and having Windows 2000 on C: and Windows 98 on D:.
That would put Windows 2000 on the active primary first partition on the drive, which would more closely match the configuration of a single boot system.
Anyone thinks that's worth a try (it won't be easy, as I don't want to reinstall both OSs from scratch)?