Personally, I would choose code 83 regardless of brand. It looks more realistic IMO. As for track, I have had no problem using Peco switches with Atlas flex track. It is not hard to shim the track heights so they mate up well. The sprung Peco turnouts are quite nice if you don't use switch...
You are doing some impressive work on the layout. It's hard to believe that is Kato Unitrack. I always remembered a toyish look to it but not so with your treatment of it.
Go back to page two and you can see he left access from under layout. I had to go back and check myself since I have been following this thread for a while now and didn't remember myself. :-)