I see NO evidence of any pathogens in your system. In fact, that last pic shows very healthy plants!
I'd advise the following:
-Avoid allowing air-pruning to occur. Run Cannazyme if you see evidence of dead material in your root ball.
-Those wrapper things hold more moisture than you want and you might consider
'planting' the peeled cubes in a bed of hydroton next time.
-Drip-to-waste irrigation for rockwool is a good way to go. You can set the drip rate and timing to allow for drying between waterings.

Use a 'zyme product to clean your system. You don't have to replace the pump. If the hydro shop guy told you to do that, smack him! Lol! He's trying to get you to spend $$$$! Run the system with no plants, with a high dosage of peroxide. That's going to clear up bits of organic material that could rot.

You ever consider going to Hydroton in quart or even gallon pots in your flood n drain? It's MUCH more 'airy' than hydroton and you don't get that slow drying thing going on. Just a thought. The local hydro shop has a display of catnip, peppers, and some purple-leaved ornamental growing in just that arrangement. It's quite efficient, and for how dirty the whole thing is (dead leaves, muck, etc) all the plants are extremely healthy. Goes to show how resilient plants are when their roots get enough oxygen.

That deficiency appears to me to have been an iron def. Not bugs or viral.