Mac is probably the only company that make long tubes for AOD. You can use AOD on a 5 speed but you can't use 5 speed long tubes on an AOD. The reason is the AOD bell housing is to wide. The AOD long tubes 02 sensor are on the outside of the tubes while the 5 speed are on the inside.
If it is a fox body then the shorty header setups are exactly the same for auto and 5-speed. Longtubes are a different story. MAC, Kooks and a few other select companies are the only ones that make longtubes for an automatic. With longtubes, you will have to get a matching H-pipe (BBK--->>BBK) to get everything to bolt up unless you have a custom H or X made for your headers.