First off, you DO want to boil the water you add to your priming solution before you add the sugar. Doing this will force all the oxygen out of the liquid and will help you avoid staling. It will also kill any bacteria in the water; my rule of thumb is to boil for five minutes, let the liquid cool slightly, and then dissolve the sugar.
I'm also not sure why you're MORE concerned about the bottles with MORE air-space? I'd think they'd be the safer bottles. Regardless, why did you put them into a sealed box? They're only going to become MORE unsafe with time. If you think they're unsafe to open, then you need to find a safe way to dispose of them; make sure that you're wearing LOTS of protection, including eye protection, when you do it.
With respect to your FG: don't worry too much about it, there's not a whole lots you can do now. Moreover, hydrometers are calibrated to be accurate at 60F, so you were probably close to your target FG anyway.