Does the other valve cover have a PCV port on it? If so, just use that instead.
So your oil cap would be sealed, and the pcv port on the other valve cover would go to the TB... and PCV port on the lower intake would go to the upper.
Otherwise, look at Mr Gasket, they sell some breathable oil filler caps - however, the after-market valve covers I was going to use wouldn't allow for their item #2045 to fit beneath the upper intake.
For now I'm just using the stock valve covers.