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Just like you'd lengthen any electric wires, you splice a piece in. As far as running the headers with the side Gibson's, I would imagine it'd be fine, the only problem I could see is by the time you have the length of the headers and the cats, Y, etc, that you may have to run it to the side after the rear tire instead of in front of it.
But you'll see when you go to removing and cutting stuff out and replacing components and go to welding everything on where you'd have to run them at...
When I did my pacesetter long tubes I left the cats off and extended my wires to my O2s. I put non foulers on the back O2s and haven't had any issues for over a year or so.