The one thought I have to that, is that if the defense can't cover the pass effectively and the offense has the players to overpower the defense with a heavy pass game plan, than 400+ yards of passing should not be unheard of. At some level the game is going to be different than the NFL, because the talent of the players in the league is different and the game plans people may decide to go with can be different than what coaches may go with. So I don't think there should be artificial controls to bring passing under 400 yards. However, I would say that if the defense has the proper talent, that excessive passing ought to lead to turnovers from jumped routes if the QB isn't experienced enough or doesn't throw an accurate enough ball. Defenses should be able to bait passes in some cases and intercept them. It would be interesting to see what the talent level of the offenses that had those 400 yard passers were and what the talent of the defenses they were facing.
I am going to stay in keeping with this - but try to tilt the scales against players who may attempt to play out of balance. The plan I'm working on is that, after the first half, is the offense is unbalanced in either the run or pass, the defense will have a greater probability of calling the correct run/pass defense option. The spirit of this is to simulate the defense adjusting to a pass-heavy or run-heavy gameplan by the offense at halftime.
I have a version of this in testing and if it looks promising will try to deploy it in MFN-1 probably this week.