OK, I feel silly about #2. I looked carefully, and see now that left and right panels are labeled as such. (Why are they called left and right anyway? Why not port and starboard?)

The rest of the questions stands, though.

You're totally right to have questions at this point in your build.

If you're finishing bright (no paint), then you want the prettiest side to show.  With the planks, if they have the rabbets for the Lap-Stitch joints, then the inboard/outboard sides are pre-determined.  Otherwise, use your judgement.  If you're painting the whole thing, then it doesn't really matter. 

Yes, lay your bottom panel across two sawhorses, approximately 1/4 in from each end.  This will establish the rocker, then the stitching holes from the garboard panels will line up with the bottom panel and the rabbets go on the inside.

Hope this helps.  Keep us posted with your progress.  Here's my EP build video if that helps:

https://www.youtube.com/watch?v=DDxowqfo1B0

   Thank you, Capain! I am actually using your video and write-up as a reference :)

So I couldn't wait, and I went ahead and stitched the hull! Transoms look like a  disaster: huge gaps and nothing fits. At the same time I think that inside of the boat looks reasonable well, and the center fits quite well too—it's the ends where the boat starts falling apart (metaphorically speaking). Suggestions?

I haven't turned it over it, is it something I would be able to fix by just tightening stitches more? (I am skeptical, since I couldn't do it in the upright position.)

I'll try to attach some pictures, let's see if it works here.

Bow transom:

Stern transom:

Inside:

You'll probably have to first loosen and then retighten the stitches gradually, working your way along and giving the boat a good wriggle from time to time.  It's surprising how a small "hang up" along a plank edge will multiply into a huge gap further down.  The trick is in the gradual tightening and wriggling as you go to relieve any stress where the plank edges "catch" along the joints.

Patience is in high demand and probably short supply at this stage.  When you get frustrated, take a break, fix a cup of coffee, and sit down in the "moaning chair" to contemplate your next step.  This lap-stitch stuff is like magic, but it does take some gentling along to get things into shape.

.....Michael

   Got it, thank you, will arm myself with patience! Any more specific tricks? Do you guys find that this loose-retight dance is easier to do with the boat upright or upside down?

I would stitch the boat together right side up.  That way gravity helps you establish the rocker, which will make stitching the garboards much easier.  You should be able to get it boat shaped in a few hours.  I agree with everything Gramps says.

I've probably repressed the memories, but yes loosen/remove stitches then gradually tie it all together.  Start with the next plank's rabbet seated properly on the previous planks top edge and gradually tighten the stitches along the way.  You will want that seam pretty tight when you go to fill it later, that way all of your epoxy doesn't run down the inside of your upside down boat, which makes it very difficult to clean up.