Ah Ha---the seat cushions! Well after thinking and re-thinking, I decided to sacrifice the BACK cushion of that front couch/bunk. (The cushion that becomes the top bunk.) I had already removed the fabric and the big board the foam was on, so it was a simple matter of removing my home-made cushion cover, and cutting it into three pieces!
Voila! Since it was the correct shape, it was the best course of action for me. Now , since that piece of foam is 3" instead of 4"---I bought a 1" pad from Walmart and cut to fit each piece before making new covers.