Justin,
The difference in the tips is that the single wall will discolor with heat (gold) and the dual wall tips won't as the inner wall insulates the outer wall. Visually, the dual wall tips have a crisper edge at the exit and the single wall tips are rolled at the exit. The factory b-pipe is only made for the turbo application and won't fit with the NA application. I may make a header for a 5sfe, but it's not in the near future. We can certainly ceramic coat the header through our vendor if you wanted to send us one. The gas charged engine prop interferes with the stock turbo intake, but I'm unsure about the stock NA intake, but I would assume it would have interference with that as well.
Twos R Us - Parts for Toyotas from Club MR2 has an NATKO in stock -- though it is for use with the factory cat.