OK. You obviously need help here. Overhaul hours are how many hours you worked on the engine outside of your normal hours. Kind of like overtime hours, but while hauling a load.
The forepeak, pump and reachrod fiasco is fairly minor. Don't worry about where the water came from while the reachrod was closed since obviously whatever compartment it came from needed pumping out anyway. As cajaya pointed out, the pumps tend to turn black when run for prolonged periods with a closed valve (such as a reachrod). This can easily be remedied be having the oiler spray the pump housing with a garden hose for the duration of pumping operations. If an oiler and/or water hose is not readily available then you could simply paint the pump housing black and there would be no color change.
Good luck with your ballasting operations and E/R logs. Be sure to let me know of anything else I can help you with.