1. You cannot overfill hard tanks. But I usually fill the hard tanks after the pnp are 50+%. This ensures that the hard tanks are as low in the water as possible and thus can fill as much as possible (since its a gravity fed system)
2. For your upgraded bags, I've set mine to about 8:30 for each of my 1000 bags. This ensures its full, but not about to break your lockers full.
3. Its complicated to calculate the total time to fill and drain the hard tanks. The amount of flow through the open valve is calculated using gravity. But if you insist, here is how you would do it.
Each of the rear hard tanks is 500 pounds, which is about 60 gallons of water.
Using the Hazen Williams calculator for gravity fed pipe flow, we assume a 3" pipe diameter for the valterra valves. Then we assume about 3" worth of drop. This is the height difference between the lake water level, and the TOP of the hard tank. I'm estimating this using the fact that the exit port on the QF is at the BOTTOM of the hard tank and that difference is approx 6". Half that and you're probably fairly close.
This gives us a gravity flow of approx 70 GPM.
This results in an estimate of just under 1 minute for fill and drain.