To specifically address the original post, beginning in 1921 OOTP provides enough minor league teams to support at least one affiliate per MLB team. So I think one could simply go into the MiLBTeams.csv file and edit it - changing the Franchise/AffiliationID indicator from "IND" to a major league team ID - to where each MLB team has at least one affiliate. You'd need to do this through 1934 (in 1935, all MLB teams have at least one affiliate), and in 1937, although from 1932-34 and in 1937 the editing would be minimal, as 14 or 15 of the 16 teams have an affiliate in those years.
As far as figuring out which MiLB team to assign to which MLB team, you could assign randomly, or look at upcoming years to assign reasonable affiliations. Or, given this...
Quote:
Originally Posted by Spritze
If player loans turn out to be impossible another approach could be independent-affiliated teams.
I ran a query last year of all the independent teams and a large number turned out to be de-facto affiliated teams as their rosters were made up largely of players who were on loan from a single MLB franchise in the pre-working agreement days. Perhaps this would be a useful addition?
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... perhaps those de-facto affiliations could be used to help fill in the blanks.
At any rate, I haven't tested this. There may be other factors that could make this impossible or more-difficult that I envision.