My approach to this puzzle was to find more than one conditional process that takes multiple loops to complete, and chain them together for that sweet, sweet multiplicative power.  This machine should be 6 times 5 times 5, Arm 1 pulls a reagent every six loops, and the center of each chamber discards 4/5 atoms.

I could have made the sticks 6 long instead of 5, but if you do that then you get all the same atom out the end and that made constructing the output much more difficult.

I wanted to make arm 1 even slower, but it's causing so many problems as it is (Like, Half of what arm 2 does is just fix arm 1's screwups), and I couldn't find a way to fit it in.

Extra Note:  After submitting this, I realized you could probably do something something processing multiple sticks of length 2 but it's too late for me.