try turning the cross over pipe till it lines up right.

mine i put the cross over in the rear header, then the front header in the cross over like 1/2 way so it could clear the 2 end studs, gave the pipe a wiggle and a twist to line it up.

i also left my TB on during the install, saw no reason to remove it.

you may have to bend the pipe some if its really off. like no way it will line up. or e mail sd and ask for a new cross over pipe to be sent you you. or a full exchange.