So, I think I ran into a similar problem with my Giant Skeleton and Block of Resin project last winter. The two solutions I came up to cover the poorly cured top layer were to use acrylic molding paste from Golden Acrylics or to use this stuff:
http://www.sashco.com/products/lexel/
I went with the Lexel because the molding paste takes a really long time to cure totally clear. The lexel takes overnight, I think, but doesn't dry as hard as the paste. It dries pretty soft like rubber cement or hot glue. The really cool thing about the Lexel is that it is nearly as clear as the resin but comes out like hot glue, but it stays workable for 20 minutes or so. You shape your waves and then highlight the crests with white and it looks like foam.
Here is my giant skeleton in aspic project:
http://www.coolminiornot.com/371579 all the waves are Lexel.
Also, you can sand that extra resin down. It sands pretty easy, but you cannot melt it with a heat gun, to try that would be pure folly.
I think we need a pic of the of this runaway resin.