Cobra MC Install Question

I bought a 94 Cobra MC to go with my front Brembos and rear 98 cobra brakes. I hear the front a rear fittings are "switched". I noticed that the sizes are opposite and was wondering if this is just a matter of the sizes being different or if the front tube on the GT goes to the front brakes but on the Cobra it goes to the rear, etc.

thanks

Davin