Six months is a solid run but that crossover point is the real killer. I ran into it with Uncanny X-Men when the whole Avengers vs X-Men thing hit and suddenly my nice arc-by-arc shelves meant pulling books from four different spots just to read one story. What finally worked for me was adding one small "event" shelf that holds the crossover books loose in reading order, so the arc shelves stay clean and I don't have to tear them apart every couple years. The other trick is leaving one empty shelf from the start, because the second you fill every shelf you're already stuck. That buffer shelf is the whole reason I haven't gone back to boxes, it gives you room to grow without redoing the system. Skip the buffer and the Matthew guy above is right, you'll be stacking long boxes in the closet by spring.

The part about the rot pattern matching your old caulk line perfectly really hits home. That's the worst kind of discovery because there's no way to talk your way out of it, the evidence is right there staring at you. I had something like that on a deck I rebuilt for a friend, found soft spots two years later right where I'd skipped the flashing tape because I was rushing to beat a storm. What made it easier was just owning it fast and not making excuses, people can smell a excuse from a mile away. Your client laughing about it says a lot, she probably trusted you more after that than before. Fixing it at cost was the right call, that kind of rep is worth way more than the money.