mustangjoe02:
Call up your tuner and ask him about increasing the O2 sensor delay and, perhaps, the heater duty cycle. The O2 sensors are seeing colder gas due to the larger diameter piping. This is a well-known issues with LT's. Increasing the heater duty cycle keeps the sensors warmer (and working 'in the zone') and the longer delay helps the computer adapt to the new geometry. (The existing delay values may not be big enough with respect to the stock learning range.) With these one or two changes, the engine will idle very nicely.
HTH,
Chris