I am not entirely certain what you are asking.
I think you are first asking if you should cover the insulation on the walls. You should cover the insulation for at least 2-3 feet up from the floor, basically as high as they can easily reach while standing/jumping, because they will peck the insulation and eat it and ruin it. You certainly can cover the entire wall. I don't see a need to cover the walls with anything more expensive than plywood, they don't usually poop on the walls.
As for the floor, that's a bit tougher question. Most of my buildings for poultry have cement floors. My brooder shed has a wooden floor and I try to minimize the number of birds in there because their poop is hard on the floor. Something waterproof, or maybe a couple coats of tough outdoor paint to protect the floor would be well-advised. Hopefully someone who deals more with wooden floors in coops can chime in here. If you don't add anything, you will want a thick layer of shavings and be sure to clean them out frequently. You would be surprised how much mess they can make when they start spilling feed & water.
Your coop needs ventilation. Without seeing a picture, I can't give you more advice except this - coops need A LOT of ventilation. So my guess is, yes, it needs a window, possibly two, and maybe even another vent or two up by the roof.
Do you intend for your guineas to free range, or will they be spending all of their time in this coop?
