Excellent progress so far! I must have at least one of these for myself and one as a gift for my brother.
Will your label be opaque enough to hide the battery shadows? Just an FYI, I work with printable, adhesive vinyl. For a truly opaque, printable label you need greyback vinyl.
The bottles look great. I love the solution for the Nuka Quantum.
My only input is that I disagree on the bottle caps not being normal. I think it is just a case that the caps visible on the low-polygon models in-game are misleading. In either case the caps seem to work. See this thread: http://www.therpf.com/showthread.php?t=254385&page=2&p=3891673&viewfull=1#post3891673