And the lesson learned might be obvious for "next time..."
I have found that these steps help with a prettier - and much less labor intensive - lapstitch lapstrake joint:
Achieve seams as well aligned and as tight as possible by adjusting wires.
Tack weld well with CA glue. Use packing tape backing to prenent glue spots from running through to back side of joint if necessary.
Pull your wires. If desired, you can achieve nearly invisilbe stictch holes by filling these with epoxy/wood flour paste at this point. Use a scraper after pressing paste into each hole so that you don't leave any lumps to sand.
Back any remaining gaps that might leak-thru to the oposite side with blue or packing tape, pressed down deep into the gap.
Consider rotating your boat so that only a couple of seams are done at a time. Rotate so that the epoxy filling the seam will create the fill-angle you desire between the two planks. This will prevent some seems from being near 90 degrees (hard-step) fill angles, while others are at less aggressive angles. I think about 10-20 degrees is about right.
Mix your epoxy cell-o-fill paste - and because you've ensured you don't have leaky gaps, you might keep it a little more runny than otherwise specified - that will allow it to flow a bit for a nice smooth filet-seam.
Get two turkey basters for the outer-hull side seams. Use a partner to fill one while you empty the other into the seam. Create a nice constant fill level in the seam by moving smoothly, trying to avoid over-fill drips.
When the seam fill is partially set up to the right consistency (keep your eye on it) use the rubber glove and alcohol trick to furhter smooth the filet-seam as necessary.
When all seams are completed from the outside, remove any tape you put on the inside of the seams.
Here is something not in the book: I had great success putting a smaller fillet-seam of epoxy on the inside of all seams. There won't be any chance of run through - and the relatively smaller seam gap means that you can usse two large plastic syringes instead of turkey basters. Use the same process as for the outside, including the alcohol smoothing when the time is right. This really works well to hide and harden that inner edge of plywood.
If done well you can create some very nice lapstitch joints this way, requiring very little sanding. The time and effort put into this process is much less than sanding after the fact.
Good luck! And if testing this out means you need to build another boat, well then - build another boat!