Really? Wow! I have never ever had this happen on a stain coat no matter how much I put on it. didn't think it was possible. We'll you proved me wrong.
I wouldn't really be worried about the finish look of it on the stain coat, just the bumpiness, if it was me, I would just need to sand down those bumps and truck on with the intensifier. I don't really worry about the final look of sheen till the final coats anyway.