The 9" Style rear end has so much more to offer in the form of specialty parts and pieces than anything else currently available. one thing that I dont think anyone mentioned is the 9" has a roller bearing supporting the end of the pinion.
As far as the 8.8 ford, there are many mustang racers running them into the 8s I think that its a case of having upgraded the HP in an existing chassis, BTW Ford itself specs Strange fabricated 9" style rear ends in there Cobra Jet program cars.
