Watering just twice might be a bad idea. Your plants are young but as they get older they will take up more water and nutrients. It sounds like your setup is doing just fine. Your pH is going to fluctuate daily and it is not uncommon to have to pH your system as many as 4-5 times a day sometimes more if your nutrient solution is close to needing a change.

To answer how many times you should be watering - there is no way to really tell without knowing the system. Since you know the system best you should experiment to dial in the correct schedule that works for your individual system. A good way to do this is to intentionally over water (something like 5+ waterings a day during flowering and 8+ for vegetative growth). This is just a rough guide, but once you start to see the first signs of over watering like wilting, you know to back off by one to two waterings. Since every system is different.

ALSO, you need to account for the time it takes for the tray to drain. For our system water kicks ON at 8am and OFF at 8:10. It takes our system another 10 mins to drain completely so we go 4 hours between waterings from the time of complete drain ie: 8:20. If you add up all the drain times it is easy to see that if you go 4 hours from the time of SHUTOFF that your roots will be exposed to just a bit too much water.