An update to my issue. After I forked around with the SY1Q files, it was working, or so I thought. Then after I imported all of the shiptos, I did a lookup again and it showed ALL of them in the lookup. EVERY LAST ONE for every customer, no matter what customer I chose. If I did a partial lookup, though, it worked OK.
SIGH. I put the SY1Q03 and SY1Q04 from my system onto their system - still happening. Reloaded MAS. Still happening. Finally I looked at ALL of the SY1Q files (1,2,3,4) and found that all of them had extra records at the very beginning pertaining to the Shipto lookup that mine did not have. I deleted all of these records (some were B recs, some were Y recs) and then my lookup began to work as it should.
One other note - the person who had been working on this conversion before me had loaded someone's BOL mod at some time. It was no longer installed, but it left a ton of records out in various places (and files, too). I don't know how it was uninstalled, but either it wasn't properly done, or the uninstall doesn't work for poop on this mod. So I don't know if some of these Shipto recs were because of it, because in some of the files there were also BOL recs at the top of the files (B recs, Y recs), too.
But it works now and we're not even live yet - who could ask for a better weekend? (Spent exporting history files from Peachtree and importing them into MAS...)