Can you run 3" pipes after the collector on your shorty headers as far back as you can?
Then neck it down to 2-1/2" mufflers and tailpipes?
I don't have empirical evidence to back this up, but I think keeping the pipe diameter constant after the collector as long as possible is beneficial. I think it is important to not reduce pipe diameter until after the cross-over pipe at the minimum. Are you going to use an H-Pipe or an X-Pipe?
edit: I re-read and saw you are intending to use an x-pipe. Can you keep the pipe diameter at 3" until after the x-pipe?