You won't be able to run with the valve covers off. I can't even prime the pump with the valve covers off without making a mess.
I tap the hole in the head to a 12-24 and use a set screw with a hole in it. Since you can't tap with the heads on, find a piece of tubing and shove it down in the hole. I generally use .070".
Also, keep in mind that
oil pans and pickup clearances are usually spot on without the windage tray. Most of my Moroso and Aviaid stuff comes in at 3/8" clearance WITHOUT the windage tray. By the time you add the tray and another gasket, the clearance is going to be up there, and it's very possible that you are uncovering the pickup.