A lot depends on what your goals with this boat are. If you're willing to accept a workboat finish, leaving the bumps unsanded won't affect the structural integrity or performance of the boat.

If you're looking to win best in show somewhere you can still pull a yacht finish out of this by going to a fully painted finish with varnished wood accents. In that case, you can cover the seams with a cosmetic layer of epoxy/phenolic microballoon mix, which is easy to sand, and smooth it all down that way.

Good luck,

Laszlo

We found these little "riffler rasps" to be very handy for cleaning up stuff like that:

Riffler Rasp - 8 piece set (clcboats.com)

Laszlo's right; cut yourself some slack.  Less fussing about finish, more messing about in boats!  <;-)

.....Michael

   This was a constant source of worry for me.  I ended up using all of the following:

* dremel tool with the detail attachment - great when it worked, often not enough room

* Sandpaper with round rubber blocks underneath - similar to dremel tool.

* Oval regular card scrapers - requires a lot of clearance

* Lynx mini card scrapers - this was super effective, especially the oval shaped one, since it can adapt to any radius. They also came in handy for cleaning up varnish drips. Hard to spend $25 on a tiny set of steel plates but you need what you need!

but seriously consider lowering your standards for the seams :) nobody looks there when your paint/varnish is going to be so beautiful on the flat spots.

   This is probably too late for the original poster, but for people like me reading this later, I've found a heat gun plus a small-handled scraper to be  a very quick and effective way to remove excess epoxy. I think I've seen the heat gun method mentioned elsewhere in this forum, and a bit surprised that it wasn't mentioned here in particular.