Here's a couple of pictures of the problem  

https://www.dropbox.com/s/lss6m88cn1973x7/Photo%20Jun%2010%2C%207%2014%2011%20AM.jpg?dl=0

   Second picture https://www.dropbox.com/s/ehxd5ipnexu9kdq/Photo%20Jun%2010%2C%207%2017%2048%20AM.jpg?dl=0

   I think it looks like it's come in through the edge of the panel.  Is there any evidence of insufficient coverage on the end grain of the panel?

   I don't see or feel any breaks in the epoxy at the keel.   I had water inside the hull due to a leak that I've fixed.   It's possible the water came thru the interior fiberglass which was more sparsely filled with epoxy and then started feeding the end grain of the okueme.   The end grain wasn't sealed prior to fillets going in, I read a post by @Laszlo yesterday recommending that. I wish I'd read it before building   

 My question is how to most easily fix it.   I don't care if the wood has staining but I want to make sure the boat doesn't deteriorate structurally.

   If you don't see any place where it could be coming in from the outside, then you need to get at the inside, sand off any varnish, scuff up the epoxy, and seal it with several good coats of epoxy. 

You might wish to test the outside seal by putting the boat in the water, adding balast equal to your weight, and seeing if any slow leaks are observable.

The black discoloration is permanent, but you do need to get the wood dry before resealing. That may require sanding down to bare wood in the wet areas.   

 Birch2 and Mummichog

 Thanks for both of you for your response and insight. On closer inspection I found pinholes at the exterior keel joint that was letting the water in.   Had I sealed those edges during the assembly, I probably would have been better off.   Rookie mistake.  
 

I sanded down to the damp wood, which is still sound.  I have the boat upside down with a couple of 100 watt bulbs inside to dry things out for a few days.   Some of the staining got better with sanding.  Thanks again!    

I'm planning to cover the entire length of the keel with dynel and graphite epoxy after I patch the fiberglass, so I have some insurance from future dings causing more of this.

 Tim