I am working with stain for the first time on my Petrel Play build.  I have closely followed the directions in the manual and it has worked well so far.  Basically, you first sand, stain then put a coat of epoxy on the pieces.  After stitching/glue/filet/glass the inside, you use a blane to knock the corners off the seams.  The plane does surprizingly little damage to the colored panel and leaves a pretty straight seem.  Then before glassing, you touch up any badly damaged areas with stain.  My only advise is to use less rather than more when you touch up the stain.  If you have to use much stain along a seem, you might want to cover it with a little epoxy before glassing.  I did not do this and was surprised when the stain wicked up into the fiberglass over the natural wood in a couple of places.  Nothing bad and I will probably be the only one to notice,

Have a look at our extensive Shop Tip on working with stain from expert kayak builder and designer Nick Schade: http://www.clcboats.com/shoptips/finishing-tips/staining-your-kayak.html

   Has anyone tried to stain a S&G kayak after use CG glue on the puzzle joints. I have joined my shear and bilge panels and sanded down the glue spots. Seems to have cleaned up nicely. Just not sure how it will take the stain. Any experience with this?

Also it says to apply a coating of epoxy to protect the stain. Else where it says not to apply a coat of epoxy to the deck panels until just before you glue them to the shear clamps because they will be too stiff. I am building a MC 16.5.

I am certainly not an expert but nobody else has answered.

1.  I would be very leery of trying to stain any where near where glue was used.  Any glue on the wood will cover the grain and prevent the stain from soaking in.  Even sanded smooth there will still be some glue there and you will have a non-stained spot.

2.  A coat of epoxy will certainly make the wood stiffer.  All of the pieces that I stained were long and thin (see pic above) so I had no trouble bending them.  On something larger that requires a lot of bend (your Mill Creek deck?), you may consider delaying the epoxy coat until after it is installed.  Be as careful as you can with the stain during installation and do a good touch up after it is in place.     

   Mark,

thanks for your reply. I tested the glue on another piece of plywood and it stained up nicely. I stained the bottom and bilge panels last night and everything turned out fine with no glue spots. 

I did find the stain to come out blotchy due to the soft wood. Did you have the same issue. Your stain job looks fantastic. I like your puzzle joints. Mine are just the standard loops. Stain helps to hide them.

chris