Was looking at a Waggy 44 rear and noticed that they have an unusual 4 bolt flange pattern and was wondering if the flanges on a Scout 44 rear are the same as on a stock CJ 44 rear?

If we are talking about wheel bolt pattern then yes the
Scout and Jeep CJ will both be 5X5.5 where a Waggy will be 6X5.5 unless it is pretty old then 5X5.5 I am pretty sure.

not the wheel bolt pattern, I'm talking about the flange on the housing. I have a full float setup on my old cj 44, wanted to see if I could use the outers on a scout housing. (Brakes, spindles,etc.)

http://www.admotorsports.com/jeep.org/housingends.jpg

http://www.admotorsports.com/jeep.org/housingends2.jpg