It turned out to be more difficult than I thought finding the correct GAL program. The collection Greenious links to in his thread pointed to a file of all zeroes - viewtopic.php?f=74&t=5040
After some searching, I came upon a collection of files on Rodolphe's page that seemed promising: viewtopic.php?f=74&t=5040#p297426
However, I've just tested a GAL programmed with that content and it results in a non-booting black screen. Switching back to the old GAL works (in DD mode, of course).
The MSTE 1.44 floppy installation manual does talk about early motherboards needing a link to be made between U7 pin 32 and UA2 pin 19 - I haven't verified connectivity between those two yet. I don't think that would result in a black screen boot, going by discussions from 1992 on why that's fix is needed, but I will get around to testing it later.
https://archive.org/stream/Atari_MEGA_S ... 0/mode/2up
So, I'm looking for a confirmed source of a working GAL program

http://www.ebay.co.uk/itm/331868782923? ... Tags=bu=bu
/Troed