The manual is fantastic, but a few things I learned while building my NE dory:  

1. Your life will be much easier if you can get all your encapsulation coats done without sanding! No need to wash the amine blush then sand the entire boat, especially it being glued lap construction, sanding can be a challenge.  Your subsequent coat can be applied once your previous coat tacks.  

2. It may be too late for this, but, buy the non-blushing epoxy from CLC.  I used west marine and had nightmare orange peeling problems when applying my second coat which may have been a result of the blush.  

3.  A cabinet scraper will save you a ton of sanding time.  Probably the same idea as your chiseling, but it will take off the excess bulk epoxy without marring the surface of the wood.  A good sharp paint scraper can accomplish this too.  

4.  Don't sweat your joinery too much unless your working towards a show quality boat.  Epoxy doesn't quite reward good joinery and will actually bond better with a little space.  

5.  When filleting- wait until your fillets start to set up a bit, then come back and smooth them out by dipping your finger (with gloves on) in a little paint thinner and smoothing the joints by hand. 

I'm sure others will have more to add.  Good luck on your build, it's a fun project!

you pulled my bacon out of the fire with the cabinet scraper tip.  barely had to do any sanding it worked so well on the squeezed out epoxy. thanks so much for your reply Giggin 

 I'm at the tail end of my NED build (primer and under-thwart floatation). Here are some tips that I can take no credit for - but stole from others and support from personal experience. 

• Strike a straight line down the center line of the bottom panel before stitching anything. It makes centering the skeg easier. 
• Cabinet scraper. Yes. Huge time and energy saver. Learn to sharpen the edge as well. 
• Before stitching anything, trace the outside of the bulkheads onto some cardboard. Stow that away for later, when you cut floatation. 
• After putting a layer of epoxy over the fiberglass the first time - only wait a few hours before cutting off the excess. It is much easier to cut it off and keep clean lines when it isn't totally cured. 

Hi guys, just wiring the unit up this weekend.  When you all wired your transoms in, and the planks up each side, was it kind of a shit show? everything flopping all over the place, huge gaps everywhere? ive drilled extra holes and have been really careful with my alignment,  but the copper wire seems to be no match for the strength in tension in the plywood. I tried to get an angle to sand in the bottom of the transom from CLC but they just said sand a bit off and try the fit.   also the dory bottom has a big "rack" in it.  came perfectly flat  in the box.  layed perfectly flat on the bench for 3 weeks, gluyed the puzzle joint together with clamps and plywood on a gunbarrel flat strongback and then the stern end just lifted up off the bench an inch on one side.  its terrible looking.  should i just not worry about it and start correcting as i tack weld/align?   thanks so much everyone.  Nate

   The dory is not a flat-bottomed boat. As you wire together the hull, you will introduce some fore-aft rocker. Is that all you are seeing?

Ah, no, not the rocker, it is looking beautiful and correct.  The rack is a twist in the last couple feet of stern.  Also called a wind, too, I think.  It’s lookinglot better today as I  wired up the last few planks.  Only lifted off the bench maybe a quarter inch. I’ve got it  weighted now and it’s sitting nice.  Also something I’ve figured out.  I bought some 18 gauge copper wire at Home Depot and it is a lot beefier than what is in the kit, which is labeled as 18.  The 18 I bought still goes through the holes.  The difference in how the stuff holds is unreal. I closed all daylight gaps in my bow and along each side of the transom with it.   Just a better bite. When you let off on the linesman’s pliers with the stuff from CLC you get a bit of spring back, with this stuff it’s clamped solid.  Worked great for a couple tricky spots.  

If it is any consolation - yes. Wiring the transom on is super squirley. Especially solo. 

I stitched the entire NED together solo without much sweat at all, but the transom was definitely more of a challenge. I didn't have to end up using heavier wire or drilling new holes, but broke lots of wire and had to end up just going very slow fitting it in and tightening. I did have to shape the bottom of the transom like you did too. 

As for the "rack" in the flat bottom panel - don't forget that you have opportunities later to check for twists in the hull before you start with fiberglass/epoxy. Simply adding the planks may help squash that rake down. Just be sure it is in good shape before you get to fiberglassing.