Somehow missed this. It's hard, right? To really integrate, you pretty much have to expand very quickly. Or else there are just too many historical players who never reach MLB.
I do think 
https://i9s.org/wp/available-players-chronological/ should be helpful, especially if you revisit the early years.
My plan is to integrate these into the actual historical data the game uses--I had very good success with that on a limited run, and had begun to write the scripting that took the raw stats and converted them into OOTP compatible data. Those could then be merged into the game database and reimported.
That has to, I think, be the ultimate goal: at that point, the game engine is working off reasonable MLE's as it does its thing.
But I plan to do it in "sets," with the first either covering just the pre 1900 folks or, more likely, the players from pre 1900 to 1910. I've been lax on updates for a couple weeks, but if you look at 
https://i9s.org/wp/most-recent-player-updates/ , you'll see a much greater rate of progress than previously on this stuff. Fingers crossed.