your stock exhaust after the downpipe/headers will flow perfectly fine. mufflers dont restrict anything at that point.
why would you NOT get headers?
its going to flow SO MUCH BETTER and you can actually run the 3.4 pulley on more timing. dont chince out on builds.
you need an O2 sensor.
you can mount your filter right on the TB and tuck in the IAT sensor, or you can build your own little intake system.
the PCM you can either ziptie to something nearby in the bay, or you can let it flop. its meant to take abuse and water damage.