TRD_141 had a dual system on his pre-facelift car and certainly didn't lose power with it (They weren't the stockies though). However, before removing your rear muffler and putting the stock one back, I would really do the DIY ECU reset and give the car a good flogging before doing anything else. In fact after seeing my runs on Sunday and how much the car opened up from 1st to 3rd runs, this is something I'm going to do over the weekend too.