Service Honda machines the cyl. where the water port is on the KX500af's to make the port tighter to the cyl. If you look at the cyl. casting it looks like they have taken off about 10mm for more pipe to cyl . clearance as well as inverting the same port. So if you buy one of their pipes and think that it will solve that water port issue it won't.
The fmf that they sell is modded some in that area but will still need to be dented in unless you do some machine work on the cylinder like they did.
I think that the PC pipe is a better fit than the FMF any way. I used the PC cr5 pipe with the k5 inlet and then put a HUGE dent in it for the water port. I can say that is not the way to do it.
If you look close you can see the HUGE dent. Also check out the part of the cylinder that could be machined for a tighter fit.