not saying you are wrong im not that kind of guy but i do work with exhaust all day long and there is basicly two options i can se especialy after looking at pics on pypes website
1. you got the wrong pipes
2. you got the wrong mufflers (seems real odd to me that they use mufflers with inlets/oulet offset/offset when stock mopars use mufflers that are offset/center)
a real long stretch would be X pipe backwards when puting system togheter on the floor but doesnt seem likely to me since most of them are using the same angles both front and back..
good you noticed this before trying to instal atleast!
second alternative doesnt seem to far of when i think of the aproximate distance missing betwen the tailpipes
most of these systems are just made to fit transmissioncrossmember and back since headers are a nighmare fore someone trying to create a complete exhaust kit since all headers end at diferent locations