If you do the epoxy/fiberglass steps correctly, then all that is needed is an occasional coat of varnish. The last coat will need a scuff sanding with about 320-400 sand paper, and a good top coat of varnish. The longest part is waiting for the varnish to dry before you re-rig your kayak.   

   the other key things i would add....(note...not unique to a stitch and glue kayak....but applies to any high-quality kayak)

• store clean and dry after use
• any deep cuts or other significant damage should be addressed with a bit of epoxy and varnish as appropriate asap to prevent further damage.  wood core boats stain....if the injury pierces the epoxy and gets to the wood....so it should be addressed quickly.

Most important maintenance is frequent exercise!  OK, I know that sounds a little like a joke (it is a little), but best thing you can do is get out and paddle!

Enjoy and welcome to the flock.

After winter storage, I have noted some mold along some cracks at the edges of strakes and around some wire holes that I guess were not sealed as well as I had thought.

This is in a 13 year old Annapolis Wherry which is epoxied, and varnished inside, painted outside. It is typically stored under a very dry porch, in a well ventilated area in upstate New York.

I see that the first recommendation to address blemishes in the epoxy is to fix ASAP and I am obviously a bit late .  My question is can I simply dry the boat in a warm garage and sand well and recoat with epoxy, varnish etc, or do I need to try to remove discolored wood and fill with epoxy.  

It all depends upon use.

If you use it a lot it will need some attention. My boat gets scratched. Mostly minor from this or that but sometimes there is an oyster bar grounding, or a piling with a nail, etc.

Traveling with the boat on the roof rack  (weeks- months)  the sun works on the varnish and sun burns it. But most people just travel to    paddle once in a while not every day. It is just like any varnished boat surface.

>> My question is can I simply dry the boat in a warm garage and sand well and recoat with epoxy, varnish etc... <<

Yes. The discoloring probably won't all go away, of course, but the boat will be just fine.

Epoxy is used all the time now in building preservation to stabilize wood that's deteriorated but hasn't reached the "rip it out and start over" stage. The preservationists got started on it by the Goudgeon Brothers (West System.) They sold the concept based on how well it works on boats.

If you want the discoloration to go away, keep sanding. Unless you're sanding plywood where colors change suddenly when you break through layers. Then you'll need to find a suitable witch doctor with potions to bleach/recolor the damaged area. 

Here's a series of case studies on how to deal with stitch-and-glue boats as they age:

What Happens When Stitch-and-glue Boats Get Old? Part One 

What Happens When Stitch-and-glue Boats Get Old? Part Two