Disclaimer, the Holley system has the best proven fit!Get the Holley 3" system. Look at how much time I spent fitting the Pypes system to my wagon. Turn a trick or two if you need the extra $200 - beats all the residual *ss pain and frustration from working with a sub-standard kit. I have a 3.5" DS in the wagon with 3" tubes... you'll be fine.
I DM'd Pypes to see about 3" side exits and they said they have no plans to build any. Way to be a team player there!