The bottom row was especially bad, so I just removed it all. Everywhere else, the loose threads were pulled to the back, and if they were long enough I'd thread them onto a needle to finish them with a knot. But all the short threads were glued down with my trusty 'Gem Tack' glue. It's washable when dry, so i figure it would be perfect for permanently securing the threads so the tails can be clipped off. It took all day, but it's finally done.
Now I have to redo all the beading in the bottom row of embroidery....