First the seams are wetted with neat epoxy resin and a brush with the bristles chopped down. The seam here is fairly wide but who cares, I'm not getting paid for this. Plenty of thick epoxy will sort that out.
Here are some seams filled with thickened epopxy. I didn't have any proper filler when I started filling the top (vertical) seams so I used a belt sander to make some sanding dust and used that instead. This is fine especially as I am taping both sides of the seams with two inch glass tape. For the lower (horizontal) seams I used West 403 filler mixed with some 405 filler and sanding dust to darken it. We'll be standing on those seams so I want them to be strong. This photo also shows some small peices of wood used to align the planks. Those planks that were not conforming were tied together using garden wire. Mostly I used cable ties.
When the epoxy cures the ties and wires can be removed and the gaps filled.
I filled the top three seams and taped them on the inside before I turned the boat over to fill the next three seams potherwise I would have been pushing epoxy into a vertical gap and it would have dripped out. I taped these seams to make sure the boat didn't fall apart as it is still very fragile at this stage. I got two guys to help me turn it over which we did on the grass outside the house in case it fell. The above photo also shows the packing tape used to cover the seams and keep epoxy resin from dripping out.