I gave the Brother a +5 against deafening attacks because his abilities depend so heavily on hearing. My RP reasoning is that the Brother not only has extra-sensitive hearing, he also has extraordinary control over his nonvisual senses; a seeing person can close their eyes to avoid a gaze attack, and a Wyrwood Brother can "close his ears" to avoid a deafening attack, to an extent. My meta-game reason is that deafening a Brother is his Achille's Heel, and he's already lost his Monk Fort save vs. everything else, the +5 just gives him a Monk-like save vs. sonic attacks.
It could be argued that because it's his Achille's Heel, the Brother shouldn't receive a +5 bonus. I disagree, but I'll change it if the judges think that's more fair.
As for the Music in the Grain instrument bonus, I made it a "+2 bonus" specifically so that it would stack with masterwork properties. Instruments made by Wyrwood Brothers are a cut above even masterwork instruments, so to speak. Now that you mention, I think I might decrease the Music in the Grain bonus to just a "+1 bonus" that stacks with everything add something for "Wyrwood wood" that gives another "+1 bonus" that stacks.
Why would they have light sensitivity? They're blindfolded.