Without actually seeing what you have(photos?), kind of difficult to do a really good "recommendation". There are hinged master cylinder covers available that can be screwed to the wood or you can make up your own using some stainless steel or aluminum and short length of piano hinge. Then you can recess that filler below bed level. I prefer aluminum as the tools I have wont work SS easily.
Another choice would be a pick up truck bedside filler. There are a half dozen here.