If the big areas look OK, perhaps everything is OK. Post some pictures of the places that bother you, and I'm sure you will get some useful advice about how to handle them. The best way to trim off the excess fiberglass cloth along the edge of panels 1 and 2 is to do so with a box cutter after the fiberglass has hardened slightly but while it is still flexible. If you miss that window and let the fiberglass harden completely, the job is much harder but can still be accomplished with other techniques and tools.

Relax . . . and post a few pictures.

   I've now got a picasa web album with the blemishes and some other stuff. You can see I'd started to sand some of them inspite of the warnings not too sand into the glass. It's not catastrophic, I do want to do as good a job as possible. Let me know your thoughts please!

   Well I should post a link! 

https://goo.gl/photos/sa1vFJq53S7resh49

Thanks for looking!

Fortunately, most of the blemishes are right up by the bulkheads. Those will be covered up by the thwarts and flotation foam later in the build so forget about them. Sand them enough to remove sharp edges and huge lumps.

You do have a few minor problems on the edge between panel 1 and 2, but I'd ignore those problems until you have applied the rest of the interior fiberglass. You'll find new problems cropping up as you do that, and they will take your mind off the old problems! The big thing to watch out for is little bubbles that tend to form as the epoxy settles into the cracks between panels. Come out to the boat at roughly half-hour intervals after applying each new coat until it is dry to the touch. Pop the bubbles with a foam brush or chip brush by very gently stroking the surface.

I recommend trying to smooth out all the blemishes just before you apply the final coat of interior epoxy. Let everything dry for four or five days before starting to sand. 

I think you are coming along just fine.

  Thanks!

What do you mean by rest of the fiberglass? I thought I was done fiberglassing. 

Also why do you suggest waiting so long to sand?

You are through putting on fiberglass cloth, but the entire interior and exterior of the boat should have at least three coats of epoxy coating (sometimes also called fiberglass -- at least by me). The epoxy takes quite a long time to fully cure. If you start sanding it too early, you'll just gum up your sandpaper.

You can apply successive coats of epoxy on successive days as long as you don't want to sand between coats.

You can read through the blog I wrote about my build to get a sense of how I timed things and confronted challenges. My boat turned out very well -- even though it is not a piece of furniture or a showroom object d'art.

http://lakenorforkadventures.blogspot.com/search/label/Chesapeake%20Light%20Craft%20Northeaster%20Dory

I was a first-time builder and made my share of mistakes.