Just figured out a way to automatically switch Ion beams between emitter ports. Lets you add redundant focusing crystals for tracking targets and/or allows for a massive expansion of the ion cannon array firing arc. 
Ion ship with over 300 degree firing arc.
Been there, done that.
https://forum.cosmoteer.net/d/11984-ai-issue-with-free-floating-medial-ion-prisms
Your ship will not work properly except under user control because of a "wontfix" bug in how the AI understands weapons.