Since none of the true experts has yet responded to your query, I'll take a crack at it. I, too, struggled with varnishing on my recently completed Northeaster Dory. I wrote about this in some detail in my blog Lake Norfork Adventures. The relevant entries are in January and February of this year. 

You'll see that I benefited from watching a couple of YouTube videos about varnishing technique. You can see them here and here.

The most unusual conclusion I reached was to try "hot varnishing"-- i. e., successive finish coats of varnish without sanding between them at all. I waited for the varnish to be dry to the touch but not long enough for it to be dry enough for sanding. This kept me from sanding through any spots and seemed to give me the best finish coat. I've been subjecting the boat to plenty of use and abuse for the past five months and so far my varnish has held up very well -- no signs of pealing or chipping.

You mentioned some areas where the varnish remains dull. Those may be "holidays" -- places where you just didn't apply a sufficient coat of varnish. It can very very hard to see them as you are painting so you may want to recruit a helper who can "boss" the job by shining a light every which way and craning her neck around and bending and stooping and generally pointing out every little flaw in your work. A coat of varnish has to go on very rapidly, but it also has to be smooth and complete. 

   Thanks Birch2.  I am going to give the hot application a try.   I have had similar thoughts.   After applying a thin coat of varnish, am I just sanding most of that off?    Will let you know how that goes.  Again thanks.

   Birch2 is correct about the light. You must have a reflection from the light as you are applying the varnish.  More light the better. Above the work at a low angle.

Brykalaero.