I'm WinDumb and I admit it!

[Waccoon]

OK, I reflashed the BIOS as detailed on the ABit ancient mobos (BX6) website.

Ah, good.  Other people should note that if you can't upgrade the BIOS on your motherboard, a cheap hard drive controller (like the SIIG ATA100 PCI card), will fix the problem.  The computer uses the BIOS on the PCI card, rather than the mobo.

Windows 98 has a limit, IIRC it's 35Gb ish

Per partition.  Make 2-3 partitions and Win98 should use the whole drive.  FDisk sucks for this, though.

Win98 came up OK but when I tried to format Drive D: it said it was only 1Gb!

BE CAREFUL!  Win98 might have gotten its remapping confused.  You don't want to format the wrong drive.

Never format a drive until after you partition it, not even for testing purposes.  PC BIOSes get drive letters confused easily, and Windows98 just uses whatever letters the BIOS has assigned to the drive.

Here's a few programs to try that are pretty small.  I haven't used them, though.
http://www.mecronome.de/xfdisk/index.php
http://www.23cc.com/free-fdisk/

[Waccoon]

This is a 'limitation' of the M$ boot loader

It's a limitation of the PC BIOS.  The PC architecture has changed massively over the last decade, but the PC BIOS is still written around assembly language and hardware offsets for some stupid reason.

A boot loading partition is only really needed if you multiboot the machine.

I'm glad those programs worked!  I myself use Partition Magic, but then, I fix a lot of computers and need the more powerful commercial tools, including those that support OS/2.