The Dougs do not align with the crossmember humps. I have never seen a set that does. One reason I imagine is that they'd be impossible to install without dropping the motor. Otherwise, fit is perfect and starter access is very good. They have to clear the floor so that and the collector size dictates how low they hang. I don't think they could do any better in that area.
I'm building my own exhaust with 3" tubes and when I made the pieces through the crossmember from the collector I did it while the engine was out and I built in a 1/2" clearance. So they'll hang low because they're 3" pipes - but for no other reason.
You can see the extensions off the collectors here. When I made them I installed the trans and crossmember.
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