Pete,
I was presuming that nothing would be done with the pilots, rather it would be a wholesale swap. Essentially everything from the walkway down would remain untouched, as well as the handrails. And everything should be painted properly already, presuming no major distinctions between the Southern units and S&A units.
Based on the Atlas parts diagrams, there doesn't' appear to be a difference between 2-rail and 3-rail fuel tanks.
