No mine did not have stock y-pipe it had been cut and made duals but the way I see it if you have manifolds regardless of what they are hooked to, then these bolt in place of manifolds so that should work with stock y-pipe or whatever, mine worked great.
The only way ball end is going to leak is if they have a bend or dent in the ball or if the pipes are not laying halfway straight on them.
Mine may have a 3 inch bolt flange at the bolts, like a 3 inch header but that ball end tapers way down.
The ONLY time mine leaked was when I lost 2 nuts holding them on, then they leaked at the collectors.
I would not want to tellanyone wrong or something that wouldn't work, but from the way I see it I would definately think if they replace manifolds they'd work fine. Mine worked great and I'vwe never had a problem with them at all.