>>>>>>>1. The panels are now glued. The manual seems to imply that all the side panels have clc rabbet cuts in them, including the number ones, but my number one panels have no rabbet cuts. The drawing in the manual showing assembly of the # ones to the bottom panel looks like the number ones don't have rabbet cuts. Should they have them or not? >>>>>>>>>>>>>>>

There are rabbets only on #2 and #3 panels.  With fiberglass inside and out, the #1-to-bottom-panel joint is stronger without a rabbet.

>>>>>>>2. I'm cutting the gains in the #1 and #2 panels on the part of the boat that will be on the outside. Any advice before getting carried away?>>>>>>>>>>

Make sure your rabbet plane is sharp as the blazes, and don't fret because you can make a godawful mess of the gains and it still work out beautifully.  (So says the builder of 50+ Skerries, speaking from experience.)

>>>>>>>>3. I messed up the bottom panel a bit. It looks fine but that was the first one glued and I only tacked down one side. It must have shifted a tad and is out about 1/8 inch from linear. Is that going to be a problem - any advice there?>>>>>>>

1/8" isn't enough to notice in that particular boat's assembly.  I would proceed without changing anything.

Thanks much - that's a relief.

Those gains take a little while, but they are turning out!

Paul (PDB)