If you are concerned about fumes, E6000 is definitely not a good choice.
330 epoxy has only a very slight odor and I never really notice that when using it in lapidary. You wouldn't have to be precise in amounts or mixing, and it's OK if the tube threads aren't wiped that well.
Just roughen the surfaces of the magnets and bottle caps with a couple of quick strokes on sandpaper. 330 has a working time of 15 minutes and hardens in about 2 hours, with max strength overnight. Or you can fully cure it in 10 minutes under a 100W bulb at around 6 inches.