Of all the Bloody Problems...

I just had my Thrush Turbo bolted on, and my manifold gasket goes. $160 later, the y pipes have been dropped and the bolts replaced, BUT, the mech tells me I should replace the pipes at some point. So, I order a 2" high flow cat, and get to replace my entire exhaust system. Question is, will the new 2J piping conflict with the fact that I just had a 2" muffler bolted on over the weekend? I don't want to create a new bottleneck after fixng the one I used to have!