Is there a difference between the front and rear rotor housings on a S4 T2?

 

yes

 

Really, would anybody happen to know what is different?

 

the rear housing has the water passage for the turbo water feed line.

If you have two front housings, you can still use them, you just need to figure out a way to get water to the turbo. If you study the cooling system diagram...there are a few places you can tee into to get water to the turbo.
-a

 

The difference is in the passage that feeds air to the exHaust ports from the ACV.