Careful use  of a rasp or paint scraper can smooth out the blobs. But "careful" is the word! If you get exuberant or inattentive you can easily put deep scour marks in your lovely plywood. (I've had to just live with some such scratches.)

When puzzle joints are not level, you have two choices: 1. You can use the heat gun to soften the epoxy, take the joint apart, and start over. Or, 2., you can sand the panels down to level. Sanding is not the way to go unless you plan to paint your boat. It doesn't take much sand to cut through the top layer of playwood and expose the cross grain beneath, which won't look great if you use a "bright" (i.e., varnish) finish. If you do choose to sand the joints, the plywood will also end up somewhat thinner and weaker. That's easy to fix with some fiberglass cloth, but it's something to keep in mind.

Using the heat gun to help remove blobs on an otherwise level joint might work, but it will soften the epoxy within the joint so there is a risk you could turn a level joint into an unlevel one.

For the blobs on the level joints, sometimes a good, sharp chisel, wielded carefully, will shave them off neatly.  If you're nervous about that, we also had success with using a very small block plane (about an inch wide) to shave things like that down without accident.

As for the unlevel one, it looks like the offset is about the thickness of the veneer, so Birch2 is right.  If you level it, only paint will hide it.  Personally, paint or no (I'm not fond of varnish over plywood, myself), I'd try to separate it and try again, mostly to make sure it didn't bend unfairly and cause problems that way when wiring up the boat.

May the Brute Force be with you, but not the Blunt Force Trauma.

.....Michael

   I should add that I have used "peanutbutter consistency epoxy wood putty" to fill in depressions in bad joints. It works well and (depending on one's sensibilities) looks OK, even on a bright finish.

���I had a puzzle joint that didn't quite come out level. I was going to paint anyway so I made fairing compound also, though a bit on the thinner side. A bit of wood flour and a bit of silica for smoothness. Sanded and moved on.