good to hear that its clearing! vacuuming definitely won't hurt, and an excellent way to get water from bottom circulating- only way in my AGP!
Maintain the shock levels and filtering, and it will finish clearing!
The reason the deep end looks worse is 2 fold-
1- the "turbidity" is incremental- every inch of water adds to cloudy appearance- think about multiple layers of plexi in front of lights, each layer of plexi lets light through, but dims the light...
2- the deeper end is not circulated as well, so takes a little longer to filter out the algae once its dead!
When your FC levels don't drop overnight, and the water is clear, you can let the Cl return to normal levels and finish balancing the pH; finish adjusting your CYA before you add more acid, unless your pH is really high!