P3 timers are a bit funky, since the abilities that Lei Shen inherits from overloaded conduits occur at regular periods, so the timers will not always line up like they did in p1/p2. You have to make sure all of your ranged/healers are paying attention to diffused lightning CD.
As far as deling with extra balls:
Have people with blink/etc. run to melee instead of taking the gate in p3. It is important that they move after thunderstruck is placed though