Hi Mike, I used woodflour-thickened epoxy to fill gaps and then went back and sanded/seal coated/glassed. Next time I might try seal coating first and then going back to fill gaps; it may be less work that way. I wouldn't worry too much about color matching unless you are working with a very uniform color/tone wood. My gaps were pretty small but I found that plain Pine flour blended well. Cedar will go much darker as a dust than it will as strips. I haven't experimented with the putties yet but I know some builders have done it that way.

I hope this helps,
Chip
http://www.nwlink.com/~chips