This problem seems to be easily fixed. Using someone else's suggestion (I believe Halofan), I was able to start a 1901 league with all the 19th century results as part of the league, including the National Association, American Association, Players League and Union Association.
Now ol' Cap Anson has some 3400 hits.
Here is the simple fix:
In the ootp/data/stats file, open the batters file. Go to the column that lists the league. Using find and replace, change NA to NL in that column only. Repeat this for the other 19th century leagues as well.
Do the same for the pitcher's file.
EDIT: Here is the link I found after posting this that covers the same ground.
http://www.ootpdevelopments.com/boar...uickstart.html