I do the 'tack weld' approach. Apply tiny spots of glue between stitches, ideally they soak in between the panels and do not protrude up appreciably (or you have the same problem). Now remove the stitches, then run nice smooth continuous fillets.

On my last build I had the tack welds break at one end of the boat along the keel line so had to re-wire and spot glue about a 4' length. I think this was because I removed the wires working towards the end. When I removed the last wire the glue spot next to it let go - then with no wires to hold the next spot let go... bang, bang, bang, for about 4'. If I had started removing wires from the end the break would not have been able to propogate along the panel. But don't be put off - it is amazing how well those tack welds can hold - I have even lifted and moved the hull around - carefully! After that breakage though I went over the entire hull and made the tacks a bit bigger, more of a 1/2" run, than a spot.

   cheers Dave

I have been considering the same issue for my shearwater build.  I had originally planned to leave the stitches in because i like the way the little flecks of metal look in the stitch holes. But i also want to use smaller fillets to keep the weight down.  Maybe I'll just squirt a little epoxy in the holes, let it cure and break the wires off on both sides.

I also tack-welded. I actually tapered the panels slightly more than the diagram called for. This gave a small v-shaped recess on the inside of most of the joints, which fills up nicely with tack-welding-consistency epoxy, sort of a mini-fillet. I also found the sryinges to be more trouble than they're worth, and found it easier to just dab it in with a small paintbrush.

Leaving the stitches in is an obstacle to filleting. You will find that some fillets will be deep, and others shallow. The stitches will really be in the way of the shallow ones.