I searched but didn't turn anything up. How do the 5/6 ports work with an aftermarket intake? Are they removed or what?

 

No, they make the same intake openings as the factory intake manifold. See down in the middle of this page on this link for the 6 port weber intake manifolds to better get a picture.

http://www.mazdatrix.com/r-idamanifolds.htm

 

I think it depends on the type of aftermarket intake you are using. If you use a one piece unit which replaces the stock upper and lower manifolds like the one RB supplies for their Holley, then you need to remove the 5th and 6th port rotating valves. If I recall correctly, the RB instructions omit telling you to remove them. If you are only using a replacement upper manifold like the ones available for a Weber, then you would leave the valves in because they would still be actuated by the stock lower intake.

 

If the lower intake manifold is replaced and not just the upper, you lose the aux port sleeves which means they are open full time.