Well, I have used West Systems for the mold and parts. Wax and PVA for the parting. Wish I had the laser for cutting the parting pieces! For the gel coat I use graphite mixed with the epoxy for the first layer. It has it's advantages, and disadvantages, it doesn't spray, has to be brushed on, so I have had bubbles form in the mold. You might want to forget the tooling gel, and use a dye for the first layers instead and see if that helps, or try mixing graphite in the first layer.
Is it possible that the polyester is getting too hot when curing, and that is what is affecting the gel coat?
Here is one I am prepping to mold, cowl for a Hanger 9 P-47 150.
This is what it used to look like,
Here are a couple I made a couple years ago for a CG Chipmunk and TF P-51. the Chippy is the first one I ever made and didn't have enough graphite for a full tooling coat. The second one I got the WS Graphite, and Collodial powder, worked much better.
All using West Systems. I am going to give Total Boat a try this time, half the price of WS, but same mix ratio and set times.