Basic stain instructions here:     https://www.clcboats.com/shoptips/finishing-tips/staining-your-kayak.html

Definately stain the panels before stitching and glueing the boat together.  If the Mananuck manual calls for the edges of the panels to be beveled prior to stitch & glue, then I would stain after beveling.  That way any little nicks and tear ours won't show.  Definately coat the stain with epoxy before S&G to protect it during construction.  You will still have a little stain touch up after the boat is together.

Not sure about boats, but in the furniture world, staining is done after all machining processes are done, often prior to assembly.

 Depends....

Anything involving stain needs to be thought out well in advance.

Any machining / tooling after staining will require touch-ups;

Anything applied to pre-stained parts likely will affect how stain is absorbed;

Stain choice and finishing materials need to be 100% compatible, otherwise risk of delamination is significant. This same applies to structural considerations when pre-stained parts will become structurally bonded during construction with whatever adhesives have been selected / suggested.

i use a lot of staining on my boats and would echo the points made above.  what i would highlight is this:

• use only a stain/dye such as Behlen Solar Lux (sold by CLC and other fine woodworking shops) that the building community has confirmed compatible with epoxy.
• surfaces you apply a stain to are very sensitive to anything that is on the wood before the stain is applied.  so for example, if you have some epoxy or glue drops on the wood and stain over it, you will often get a discoloration even if you have sanded the drop off prior to the staining.
• the techniques, as mentioned by SP requires a lot of thinking in advance and is a function of what effect you are trying to get.   so you might approach it differently if your intention is to stain the whole boat a uniform color vs just some panel and not others, or staining a piece of single panel/piece, or staining with multiple colors.     anything you can tell us about what you're trying to accomplish can help.

h