Also the inspection photos show some of the roof joists look like they're partially cracked.   

Finding a solid property management team is crucial, especially when managing from out of state.Having everything you need under one roof can really make a difference.

My tenant mentioned that there was a leak coming from the toilet in April.

Other exclusions are roof replacement, anything requiring a permit, exterior painting if more than 5% of surface, "maintenance related to the garden, lawn, or landscaping," anything covered by any of the various required insurance policies, etc.

Hire a Architect to provide drawings with a lot of details such as existing house elevations and floor plan, proposed elevations and new floor plan, roof, wood deck, addition, etc.

First is from roof along 3rd floor ceiling and I could not isolate source on leak test.

An egress roof window would get you into the roof which could get you over to the second floor stairs, I'd have to add a few more stairs but that would be easy. 

New roof, new siding, new plumbing, new electrical system, new kitchen, 75% of windows are brand new and fully renovated house.

I'd try to go up on the roof and look to see where the water is coming from.

After discussing with my contractor, since there is nothing backed up or leaking and the toilets and sinks are draining properly, there is nothing to repair or replace at this time.