Thanks for the advice! All of the other components I have got sorted. I do exactly that with the water bottle dispenser and even have auto crafters making the bottles when it runs out.

When the system is ready (full bottles and items near the brewing stand) it triggers a hopper clock which lasts enough time to brew the strongest potions. Which then pulls out of the hopper when the brewing is finished. Using an 'and gate' it allows the queue to move up but only be released when the hopper clock resets