Were the task mine, I'd be tailoring splines to the seams adjusting the thickness as required to bring the seam width back to a more acceptable one. Glue these splines to the lower plank only, and hold them in position with tiny wedges while the glue sets. These should ensure that the seams taper to a relatively tight fit halfway through the plank thickness. I know that it's a fiddly job but the boat is worth the effort. You can use this method for the full depth of the hull. In the case of the garboard seam, the most critical one, I'd glue the spline to the plank rather than the keel. I'd use Oregon Pine for the splines, as it will hold on to the glue better than Pitch Pine. The usual caveats about gluing to Pitch Pine apply, too. The first caulking should be done with a light touch; just enough to get a seal and to harden up the planking to a cohesive unit. You can harden the caulking after the boat has been afloat for a season, if you think that it needs it. To paraphrase an Old Saw, "if it don't leak, don't fix it!" Peter.