I am the owner of a Canadian 5-cylinder FWD 4000s... Recently, the auto transmission on my car decided that it was time to go to Audi heaven... I have called the various scrapyards in Vancouver for a possible donor replacement, but to no avail... although automatic transmissions for 5000s of the same year (1986) seem plentiful... I have checked the specs, and aside from the reverse ratio, the other ratios appear to be the same... does anyone know if the automatic transmission between the 5000 and 4000 series cars are interchangeable?

While I cannot guarantee it 100%, I don't see that it will be a problem for you.
I had purchased a used manual trans for use in my CGT, and it was physically identical outside. I don't see why the autobox would be any different.