Using lacquer thinner to clean the area you want anything to stick to will help a lot with the bonding. No drying to worry with either, blast of air and its ready, and even thats not needed.
I would get something better than JB though, some of the marine epoxies might be good(Slash Zone from Z-Spar is good).
But I have to agree, knocking down any high edges and getting on with it would not be a bad thing either. All though I willl have to admite, it would bother me if I had to look down at my table with holes in it.
Ofcourse you could machine/grind the whole table. Or drill & plug it with a slug of cast iron and then machine/grind. If you do epoxy be carefull of sanding down to far and causing a low spot around the spots. r
Jess
GOD Bless, and prayers for all.