My solution to this problem was a set of 3.1 ROMs from a trashed 2000 on eBay, plus a ROM switcher. Mine works by holding CTRL-A-A for a few seconds, which toggles between the two ROMs.
Having said this, WHDLoad is so good that it's rarely been necessary for me to use the 1.3 ROMs at all. For example, I can now play Archon (my favorite game since my Atari 800 days) on 3.1 ROMs with my 030 running, and the commercial release of the game never ran on anything but KS1.2.
You do need an image of the KS1.3 ROM to play a lot of the WHDLoad games, but since I had the actual ROM, this was easy. ;-)