Here's the page on the website dedicated to the Starship Cube Master, where you can also find the download and instructions on using it with your own copy of Minecraft: http://www.pixelships.com/misc/sscm.html
Feel free to replace all the buttons with pressure plates if you really want to. :P
When I said the real Enterprise doesn't have bathrooms I was more-so referring to the fact that you never see them. Supposedly, the Enterprise-D only has one, at least according to Riker. ;D
Also, when I say "no way to do elevators in Minecraft" I'm mostly referring to the idea of traditional elevators. I know it's possible to use pistons to make elevators of a sort but it's not exactly the same thing. ;)
I think the bussard collectors can actually collect particles for later use in Star Trek lore, not just convert them to energy. Not sure about that though.
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