There's a guy on you tube who shows how to cut the glass bottles or in our case tubes, with almost a perfect cut. If you get those cutters (I've seen them on lab equipment sites) for cutting tubes (they have a cradle for the tube) and cut a single straight line around the tube, then slowly pour boiling water over the crack, then run it under cold water, it should pop apart nearly perfectly straight. I've got 12 feet of tube coming in that I will be trying this with. I figured I'd do one segment of tube at a time, cutting a single piece, breaking it off, then cutting the next. With a bucket of water in the sink to catch the falling pieces, I should be pretty safe.
As far as caps go, if you want metal ones done spec, then you'll probably get it cheaper locally, as I have found this to be the case with most metal work I've needed done. Delrin is a good possibility, as are the rubber ones, and you can get premade ones from chinese manufacturers, you just have to contact them with your sizes. I am in contact with one asian place that will do a clear silicone grommet too. I'm not sure how that would be with reactivity with juices though.
If you want to melt the ends for a rounded finish, you can use a basic propane torch you'd get from home depot, you can even do some basic glass melting with it if you wanted to decorate the outside, though it's not ideal for that type of set up. You can also use a micro torch to round the edges, but the bigger torch is faster.