[RidgeRunner]

I have had that happen before. Not a good situation to say the least. I was sure that my surface was clean and prepped (ground with 40 grit on grinder). The glass and resin were new and everything was dry. I believe the substrate(plywood) wicked the resin out of the glass before it had time to kick. Moisture can also cause the glass to fail to properly wet out but if you are sure it was once clear like the surrounding areas the super soaking capacity of the plywood might be to blame. Try to coat the area with resin before laying the glass in. If you were using poly resin I would say to mop on a hot coat first by thinning the resin with acetone and adding a little more hardener to enhance penetration and soak the plywood before proceeding with glassing. I am at a loss with epoxy.
On vertical work I have seen the resin run out of the glass before the resin kicked up it is not for the faint at heart. If you catch it early enough you can recover. (ie get frantic with the bubble popper and resin)
In your case, it is really about sealing the wood and it is structural. There are a couple solid milky areas that need to be redone IMO.
I don't think you will ever get it to be clear and free of air. Prepare to itch. Good luck.