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Is there any reason why it wouldn't work? I could see where vendors wouldn't want to because they would want to use the generic mass produced version. But for a 1 off application why not. You would have to custom build the outlet piece anyways. Its just a different bolt pattern for the flange.
That is unless they make outlet ports for these that can be found easily and cheaply, but I guess I haven't really seen those.
the 03'-04' cobra has a blower case specified for the application. Because ford also intigrated an A/W intercooler into the application. So you'll notice the blower for the Cobra's as a flange around the base of the blower. This allows it to be bolted to the lower section of the intake which houses the intercoolers heat exchanger.