The problem with using stir bars is that then you have to fiddle with each bottle to get the bars in and out. What if you used a bunch of small electric motors, set up in a grid, each powering the rotation of a metal dowel with a propeller-shaped stirring attachment. They would all be attached to the underside of a table, and another platform (with holding spaces for bottles) would hang below this. You would be able to raise and lower the bottle holding platform to allow easy placement of the bottles, and cleaning would be as simple as replacing juice bottles with cleaning liquid bottles (water or whatever ya wanna use) and running a rinse cycle. The whole system would give you the ability to run a batch of bottles in a "set it and forget it" manner, and keep you from spending time setting up the stirring of each bottle individually. I can explain the design further if you like it, I'm on my phone now haha