Your DWV plumbing is the same layout as mine. I think later they made that run more diagonal (and then maybe later than that they straightened it again). The way it is, it's super easy to make a box for that and then reclaim all the space above it (which was lost by the original design).
I'm not sure about the door leakage. Mine has basically been missing the weatherstripping for awhile and even in deluges no water comes in. You might take a look at the caulking around the top of the door on the outside where that little "hood" meets the roof. I guess there are lots of places it could come in, but I would think that when you find the right one (or ones) it will be obvious due to some trail of evidence. What I mean is that I can't see a chronic leak leaving no sign once you dig in. It can originally appear far away (because water travels), but once you dig into the leaking area there should be some signs.
Boy does that compartment look better now!
PS: Funny on the rust tool outlines: It's like the "bad" version of those super tidy tool boards that have an outline of each tool to show where you are supposed to hang it up
