There are numerous threads on here re Negro League players, which - to put it mildly - are problematic within the OOTP context.
I'd suggest you go a-hunting and bower-bird the info you're after. It's a topic that's fairly well covered on these boards. I've semi-successfully added some NL players to my saves following the info I've pilfered from them.
Seamheads is another invaluable resource, not to mention being right up there with the best baseball websites going around.
Re other leagues such as Japan, as far as I'm aware they aren't in any of the OOTP databases so it would be a manual process.