This MIGHT be a bit polarizing, but I feel that the more you play, the more weathered the parts should get, making a less clear sound and lowering the quality. This could be beneficial to players who WANT a specific sound out of their organs. Repairs could be done with planks for the windchest via right-click, and copper for the pipes also via right-click. I simply believe adding some upkeep to the instruments would add another layer of deoth to the mod.
#Pipe/windchest durability
uncut notch
charred fable
You are right, this is very polarizing. But I do also agree that some people might want a weathered sound in their organs. Since the pipe bases are made of copper, why not have them oxidize over time when placed (with no pipe attached)? You can then use this oxidized pipe base to craft the pipe you actually want.