Leave the refugium on 24/7 that should sort that problem at the moment. Check the water chemistry and make sure alkalinity is on the higher end of the range say 11-13 (NR 8-13), but the fact that it is low in the morning and highest in the middle with a slight fall in the third reading later at evening/night, it sound like CO2 issue. Also surface aggitation have plenty of this. The slight dip at night is possibly explained by people in the house and if corals in the tank slight photo inhibition. The former is the most influencial though.
Hope this helps
Regards