Sounds like it is time to decide whether to go with the stain or not.

If you go without, it is easy enought to use epoxy thickened with mixtures of cab-o-sil, wood flour and saw dust to fill the gaps.  If you experiment a bit, you can find a mixture that matches pretty closely, and will barely be visible on the finished boat.

If you decide on stain, I would start by reading the other stain related thread that is currently active.  I have not used stain over strip over a strip build so am unsure what the best approach would be.  If it were me, I would use some scrap strips to build a "test" section.  Try filling gaps with wood putty and various epoxy/wood flour mixtures then sand and stain to see what works best.  You may want to try adding a bit of stain to an epoxy wood flour mixture and see how that works.

Does anyone know if there any issues with staining the epoxy/wood flour mix?  How well does that accept stain? 

I'd like to have the option to fill the gaps with something that will allow me to decide whether or not I want to stain after the fact.  If the fill looks good and matches the natural wood well, I might leave it alone... but if the gaps look out-of-place, then I want to be able to stain it and color match it better.

Thanks for everyone's help!

in reading your question, as i understand it, the intention is to stain it a dark color if you stain it. my first comment is dark stains hide imperfections (staple holes and gaps) much better than natural or light finishes as these areas almost always show up as dark spots absent staining.

so some epoxy with wood flour will be just fine.  my personal preference is a technique i got from one of the build videos and just uses wood glue in the gap and then sanding over the wood glue (while it is still wet) to blend the adjacent woods' saw dust into the gap (sort of color putty on demand) which holds a stain exceptionally well.  the wood glue technique also sands easier than epoxy.  the only limitation on this technique is it cannot resolve 'large' gaps.  so i use it on staple holes and or gaps  ~ 1 mm.

if no stain is going to be applied, you need to experiment a bit as suggested.  in experimenting, you need to try your putty technique (either epoxy or woodglue per above) but then actually do the expoxy coat before you call your experiment complete.  it is possible to 'match' the color prior to epoxy and find the epoxy absorbtion/application process changes the result.

fwiw....minor imperfections in the stripping add character and beauty.  just as long as the gaps are not too large.

h