This is where you may get the limp mode problem even with the stock controller. (That is where my problems started). I.e. Even if you keep the stock controller, you need to disconnect it from the exhaust to connect the new Ti exhaust. When you do that, if you don't connect it back in the same "remembered" valve position, you will end up with limp modes. The Miltek controller mitigates that, by simply keeping the valved fully open and returning "all ok" to the ECU. I think easiest path to great sound seems 3rd cat delete, stock exhaust, but then you may have emission check issues.