I was running stock valve covers with the thrickflows. I had to cave in the baffles to clear the rockers. Common problem. But since you are running the script cast valve covers, they don't respond to setting them on the lawn and beating clearance into them with a hammer.
So what are the options...
There are valve cover spacers. Shaped like a vlave cover gasket and go between the valve cover and the head. I am not a fan, I don't think they look right.
You can raise the PCV and build some baffles in the chimney, tricky part is you need enough volume so the air flow will slow enough for the oil to fall out and run back into the engine. Too small and it will just suck right on by.
Another option I have not seen mentioned yet, there is usually more room on the side of the valve cover then the top. Build a baffle and port the side of the valve cover. Done right this could blend in very nicely.
Unless it is an all out race engine that doesn't expct to live in the real world, PCV should be there. Breather on one side that lets air in most of the time, but can vent during periods of full throttle. PCV to regulate airflow to the vacuum source, shuts off during full throttle use. Vacuum to both sides is wrong and won't create the positive airflow that Positive Crankcase Ventilation should do. The idea is to keep a fresh breeze of air through the engine to pull out condensation and other vapors during normal use.