Are the forward o2 sensors close to the same location as they were with stock manifolds? If they are moved farther down stream with the long tubes it could cause a delay in feed back to the ECM causing a rolling idle like you are describing. This is a problem I have seen when modding Mustangs. In the pony car world access to tuning software is easy, the FJ is my first stab at a foreign car. I have not seen any options for user end tuning.