here is a post on adjusting the Mustang Cobra caliper pistons. You should be able to find others with more detail, but it appears that setting the parking brake adjusts the caliper piston, so now that you have the parking brake cables routed properly set and release the parking brake a few times an see if that helps.
I would also check again to be absolutely sure the rear brake lines are bled and have no trapped air.
Adjusting rear brakes - 94 Mustang disc calipers.
