The Gun Trey formations I would have to see for myself to give advice on how to stop it. What I noticed to work against stopping my run game is users that blitz their nickel back. He comes off the edge and into the backfield so fast that I'm usually stopped for short gains even on inside runs.
I agree 4 verts is hard to stop. They are most dangerous with trips to one side. Your best bet is Cover 4, or man imo. Cover 3 drop/match is ok if you have a strong dline. If you get caught in zone against 4 verts, control your LB to the trips side, and cover the #3 receiver at the snap, then fall off to the number #2 receiver. The #2 receiver is the most dangerous if you get caught in a zone. Receivers will eventually get open if the QB has enough time so try and get into zones that focus on deep routes like drop, match, or sky. This gives the rush more time as the receivers have to clear DBs that are dropping back. If in man, the receiver running across the field is who you want to lockdown.
I don't use cover 6 or 9 enough to know if they will slow down 4 verts.
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