Oh man, ok so looking at that and taking the example that Tzent used in the initial forum with Jason Bartlett. He said that if the pitcher was from 1957, the average fielding percentage for a SS would be .9609 but using the numbers on BBRef you get .9605. And for the Honus Wagner example with the 2005 pitcher Tzent said it would be .97399 and using the BBRef numbers you get .974, which is certainly close enough to be serviceable.
Even so, I doubt anyone is willing to take the time and go through each position for each season and average them if you have to manually go through and find 2 players from the same position, in the same season, one from each league, and then average their 2 fielding percentages. There has to be an easier way to do this. Knowing the best and worst fielding percentages by position and season seems to be an integral part of the new defensive system.