The compare-locales output on https://l10n-stage-sj.mozilla.org/dashboard/compare?run=132896 shows some obsolete files. Those can be removed, not going to block on that though. As a bit of background, the brandings for nightly and aurora are not exposed to l10n, they always take the en-US strings, which is going to stay that way. Thus you don't need to bother about those. Which makes me ask, is that something specific to your tool that you translated those, or just a "better safe than sorry"?
So why are brand.dtd, brand.properties located under locales/en-US/ ? I take to translate all files under locales/en-US/. Why should I make exclusion for these files? Why are they located under locales/en-US/ if they are not localizable?