When i did the fret-less conversion on my Aria i used a two part glue, (something with a bit of give in it so that it wont dry totally solid and crack under vibrations of playing, truss rod adjustments etc) so would advise against anything like super glue to fill the slots it.
Apply the glue, let it dry then carefully file it flush finishing with very fine sandpaper then give it a good lubing with some lemon oil to finish.
Then all thats left to do is give the nut a bit of a cut/file to to get the action lower over the whole board, but play that one by ear, just because there are not any frets now its doesn't mean that you wont get a buzz if you go to low !
Good luck an have fun !!!!