Rubber hoses?

Hello everyone
I would like to remove all the rubber hoses that the previous owner used.
From the transmission the steel likes are cut and there is rubber fuel line through the header tubes with a heat shield material around it.
I was thinking about using an-6 lines from the transmission and route them away from the headers to a new trans cooler that I would like to install.
I would appreciate any opinions on that.
Also I have the stock mechanical fuel pump, do I have to swap out that pump to install an fittings. the stock pump is using a flare nut which is a much coarser thread than the standard npt.
thank you
George G