Not sure if we're doing the same boss, because leveling up is pretty much inevitable in p2. Unless obviously your raid can pull 4078200 dps on the boss only and your tanks are moving the boss exactly at 100 energy while not leveling up the conduit. If you were doing that, I doubt you'd still be wiping though.
Level 2 + some energy becomes level 3 during transition. Lei Shen increases all pylons by one during intermissions.
I'd suggest disabling Bouncing first though, helps in both reducing overhead and learning curve to actually spread out nicely for them.