I actually stopped being lazy and cut the lines down below. I was bearly able to cram the fuel filter with all he AN fuel fittings in the stock filter location but it fit snug. I then ran the single 6AN line up to the fuel rail.
And not quite sure about the harness issue bit I do know the 99-02 run a different than the 03+
I would get both wiring schematics and try to figure out