After looking into this more the answer is to not use this method to create the matrix.
There is no built in way to get the "Points" back out without creating your own function.
The easier way is the way they done it here
http://practicalcryptography.com/ciphers/classical-era/bifid/[
^]
Just view the source of the page to see the functions.
They are basicly creating two list of integer to work with the x,y locations in the 5x5 matrix.