I just went through a very similar thing with my Mako project. I had gotten some bad advice from a tech where I bought my Vinylester, so I added wax to the last batch of resin I used when laying up the new outer transom skin. After talking to a few experts, I learned this was not necessary. In order to make sure the wax was removed and the surface was clean prior to bedding the core, I had to thoroughly grind the new glass with a 24 grit disk.
I was also told NOT to wipe with acetone. Appratenly, if there is any residual wax, the acetone will simply spread it around. So, after grinding, I vacuumed the surface thoroughly and simply wiped it down with a tack rag.
Sand the surface thorougly, vacuum it, tack rag it and put down another layer.