Humps, bumps, and screws ... oh my!
No worries, guys. Wood is a natural product and it'll always vary from boat to boat. Remember the old saying that the only difference between an experienced wood worker and a greenhorn is that the experienced wood worker knows how to hide the defects better
OK ... back to boats. I wouldn't worry too awfully much about the humps and bumps - you'll have ample opportunity to fix those things later ...
if it's still necessary to do. I would
not try to fix these things now, and I'll tell you why. The bottom panels are a large floppy sheet of plywood and they'll take on much more of their final shape after they are resting on (and screwed down onto) the main stringers. Apply the second layer of 3/8" ply on the bow when it's time, and do not worry about filling humps or hollows first.
As for the 'hide the defects' mentality, keep in mind that each step is an opportunity to correct anything that's not quite right from the last step. For example, before adding the chine flats, make sure the spreader bar and critical dimensions at the bow are what the plans specify. Add a screw through bottom panels to molds (towards the top end of the molds) if necessary to pull the panels into the mold equally on both sides of the boat etc. Eyeball the edge that the chine flat will attach to, give the bottom panel assembly a general look and/or measure to make sure all is square,
then add the chine flats. Just prior to adding the 'stitch welding' epoxy between ties, give it one last look .... you're not committed to anything until you've locked things in with epoxy (and even then, most things are fixable).
Later, before putting the side panels on, again ensure that the chine flats have a smooth straight run on their aft ends (as discussed in the manual) and that all curves forward of the aft straight run are fair and smooth (they will be) before you lock the side panels into place with epoxy.
It's not until after the outside of the boat has been glassed (seams, sheathing of the whole boat etc) that you stop and take a look at any remaining humps or hollows. Fairing these things out is the second-to-last thing that you do before finish coating ... whether graphite epoxy or a paint system. Once faired, the hull gets a couple of finish coats of epoxy and then you move on.
Hope that all makes sense - I'm just saying "stick with the plan and no worries". You've got to expect some variations to occur. Those molds are there for a reason, so no reason not to force bottom panels down onto them prior to putting on the chines Trust your eyes and double check a lot before locking things in with epoxy. Fair later, not now. No fairing between layers of plywood. Keep on truckin'! Looking great from this end!
Brian