To the best of my limited knowledge, the bees won't clear out capped honey until they plan on using it, with one special exception that doesn't apply here. But anyway: don't worry so much about the tracheal mites; if it's a question of either/or, treat for Varroa first - I recommend Sucrocide. If your state's program is good, give some sample bees to your county inspector and ask him to have them tested for the presence of tracheal mites (this is done for free in Ohio, I don't know about your state) before you drop the copper on a treatment.
It doesn't look anything like foulbrood, so I wouldn't actively worry about that. Please don't use Terramycin.
And lastly - it may be too late (perhaps you've done it already), but I wouldn't put any of those frames in another one of my colonies. At the moment we really have no idea why that colony died - giving their honey to another colony might be spreading something bad. Like others, I don't want to freak you out or cause you to overreact - but as long as there is the possibility of disease, you might be killing another hive. I'd wait until I had a tighter handle on what exactly took down that colony.