IF you replace the factory set up of 4 cats ( 2 each side) with 2 cats (1 each side) that are of good quality & retain the down stream O2 sensor factory placement...then you should be OK with no issues with the CEL coming on due to lean run condition. keep the pipe size either 2-1/4 -2-1/2 dia and bottom end torque loss will be minimal

as to what mufflers you wish to put on down stream from there is your choice...just be warned that flowmasters tend to drone inside the cab ....but that doesn't seem like a issue for you now...just might be a few months down the road.