This is how I see your system functioning: you start plants in an EnF system, then transplant them to NFT until harvest.
If that is correct, Just use 2" net pots filled with hydroton. Place them in your EnF w/o any other media present outside of the net pots and germinate directly in the net pots. I would probably plan on flooding about every two hours unless I find the hydroton stays wet longer than that (you don't want seedlings to dry out at all) I would probably set the flood level to about the same depth as the seeds are planted.
You'll leave them in the EnF system until roots are coming out of the pots. Then you transplant them to the NFT system.
If you want to use the rockwool, just because you have them, do the same thing only set the rock wool on top of the hydroton in the net pots and set the flood to just touch the bottom of the rockwool. You'll need to pay closer attention to the moisture level of the rockwool because it holds so much more water.

You see it correctly. We will try it. I have trouble getting hydro ton around here, but choir is common. I will find some and play with it.

Hydroton was the first, but there are now several different brands of "rocks" sold for hydro. If you can't find any of those, lava rock will work. You have to be careful with the roots on the sharp lava rock, though. And if you can't get lava rock, in theory anyway, any ph-neutral rock will work.

Turns out we are going to be near a worms way tomorrow. I may buy a big bag of hydro ton. I was disappointed today. The chior floats around when the water comes on. So it is not going to be useful in this application. I think it holds dang near as much water as the rockwool. I have one more tray of rockwool then I am going to try to switch over to chior in net cups and do away with the rockwool.

How would I test the rock I have to determine if it is ph neutral? Wash it good, put in a container with known ph water and let it sit? I like the idea of rock. The small amount of hydro ton I have tries to float.

From what I read, rock that will make your ph rise will bubble when in contact with vinegar.

My buddy is running 'Ebb & Flow' with 4â Rock wool cubes. He is following a plan of flooding the cubes twice a day with 2 inch deep flood. It's working quite good for him. Cubes needs to be maintained mildly damp and not too wet. If you find the RW getting dry on the surface, flooding frequency needs to be increased. In flowering though flooding once in a day is enough.