I think they will be OK.   On my Shearwater, I must have missed the directions telling me to tack weld the deck and hull and I used clear packaging tape to hold the deck and hull together on the outside every 6 inches or so (instead of wiring it up again).  I then applied the fillet to the inside seam and put the fiberglass tape over the wet fillets in one step (a nasty process to work inside the boat, but it was over pretty soon).  My deck overhung the hull by a few inches on each side and the tape held it in place well enough without any wire stitches.  

So, if you're worried, you could use some painters tape or packing tape on the outside to hold it together in the places that are really stressed as added insurance until you get the  fillets and glass on the inside.  I think the key point would be to make sure the tack welds are really well cured before you take out any stitches, assuming that's what you're using to hold the deck on at the moment.   

Woodflour glue is plenty strong. The strength is in the epoxy, not the filler. All the filler does is keep the glue/putty from running. As long as the filler doesn't introduce air spaces (like microballoons do), it doesn't really matter too much what it is. FWIW, I've never used cab-o-sil in any of my joints, only woodflour, and never had a boat fall apart.

As far as the stress points are concerned, Kathy nailed it. The tacks must be fully cured and stress point can be helped along. That's exactly how I did my WD12, except I used shrink wrap (no adhesive mess). It's held up just fine for almost 3 years now. Click on the picture to get to my website with full descriptions.

Have fun,

Laszlo