SpaceChem’s shortcut key for pausing

I finally figured it out. I'm supposed to use the control switches to not fire the laser until the eye is open on the pyramid. I guess this allows the particle accelerator to charge up more to hurt the eye while it's open instead of wasting power shooting at it while it's closed.

On research levels where inputs execute instantly (it's not waiting for the pipeline, etc), you can usually eliminate all SYNC instructions by just making the path length for the blue and red Waldos equal. One instance where you can't do this is if you perform a single rotation (or generally an odd imbalance of rotations), as the path length for a circuit will always be even, and rotations add one cycle.

If you just want your blue Waldo to just run opposite the red, you could just move the start much earlier in the circuit, for instance like in this puzzle (final one on the first planet)

Eliminating SYNC instructions can be much more difficult when you have reactors that run much faster than the input can keep up however. If you can tolerate some imbalance in input times and the reactants come at a roughly predictable ratio, you can sometimes avoid it by just spacing them out.