All the mushroom issues aside, WHAT ABOUT THE ROOF?? For a 5 year old assembly to be leaking at all, let alone in that many places, is nuts. Even a "builder grade" assembly should give you 15-20 years with no issues. You REALLY need to get a competent roofer / contractor in to look at the roof. Your entire house could be structurally compromised in more ways than you can imagine by a bad roof. I routinely do six-figure structural repairs due to nothing more than leaks, which lead to rot, which leads to carpenter ants or termites, which leads to beam / wall / framing failuers, etc., etc., etc.
Also, anyone who would tell you that the integrity of your roof is dependant upon caulking has NO business being on a roof. All valleys should have Ice & Water shield membrane from ridge to eave and it should be along your eaves as well. "Caulk" should have nothing to do with the equation. Go to
GAF Weather Watch for more info on one version of this product. This site also has great consumer recommendations and links to find certified installers, etc.
I agree with earlier post that there is a high likelihood of hidden damage elsewhere, that bathroom floors should always be hard surfaced, and that you should spend the few extra bucks to get in a qualified IAQ (Indooor Air Quality) company to do an evaluation. There is a chance that your homeowners policy may cover this if they feel that the structure may be compromised.
Bottom line though, it is pointless to fix anything on the interior until you have the roof redone... NOT repaired ... redone. Any system that young, that is leaking that badly, just needs to be fully replaced. Bandaids will only lead to bigger damage and headaches long term.