Yes, there's fiberboard faced plywood in my engine compartment too. Clorox cleanup in a spray bottle is my mold destroyer of choice. Ventilate if you use it inside though.
I did the PSS shaft seal when I had the engine out. This is it's second season and she's bone dry. I used to have a pernicious oil leak so I never considered a bilge pump in there. I would have had a slick leading the EPA & the Coast Guard right up to my transom. I kept absorber sheets in there and hand pumped the water into a bucket. Usually at the end of every weekend along with the ice box melt water from the bilge.
Bob