I use a piece of plywood in this space also,as the pan that i have only fits falf way.I found a 1" deep baking pan to put on top of the wood portion.If i need more humidity during lock down,i use a wick pad as used in the sportsman incubators.I have posted that idea as a possible fix in the past. I think the plywood would be a good idea in order to keep the air flow going as designed. Maybe use even a cookie sheet or large sheet cake pan or two on top, as humidity is controlled by the surface area of the water exposed to the air flow. I have the original pan in mine and it is divided into three compartments so that the humidity can be adjusted.
You are right on too in thinking to put something on the floor of the incubator. Multiple layers of plain old newspaper will work fine. Might need to lay a stick or something on top if it wants to blow around. I can't remember how strong the air flow is down there.
I use paper towels to line the trays and tinfoil in the bottom.This makes it easy at cleanup time.