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NavyHog I know you are probably going back to your old version of the spread, but I was thinking there are a few changes you could make to your Pistol offense to help a bit.
Pistol Full House would help you out a lot. A lot of your run game is hurt because Pistol doesn't have very much variety and even though your back isn't offset one way or the other, most people can hedge towards the strength of your formation. Whenever you went two HB or a HB and H-Back, I was able to hedge to the side of the 2nd back. Occasionally you brought out a weak side run, but there are just so few weak side runs in those two back Pistol formations that I knew you weren't going to have much to attack me with that direction. Full House provides a true balanced formation that you can flip to either side at the line easily.
The other thing is that you might benefit from my Weak Slot -> Full House audible package that I used in my previous offense. It takes up some audible space, but I'm not sure how many audibles you're using right now. I believe you have a true fullback on your roster that you use, so it'll work perfectly.
Base out of Pistol Weak Slot with the Fullback package (this is necessary) so your base formation is this:
-----WR----------OOOOO-----------WR-----
------------------------------WR-----------
-------------------F-Q---------------------
---------------------T----------------------
You want your quickest speed threat in that slot position. It may be a WR, it may be a HB, whoever you want carrying the ball most often should be formation subbed into that spot. Then you're basically running a play based on the alignment. If the defense is tight, throw bubble to that slot guy. If they are spread out, you can audible. I usually did 3 audibles for this series:
Full House Off Tackle
Full House Read Option
Full House Triple Option Wk
Audibling from that base formation to Full House will bring that slot player into the right up-back spot. You can snap it right when he gets there and create a small series of plays with it. It takes up some audible space, but you can do as few or as many as you want. It's really good against users because they can't possibly cover everything and you have a play or audible that can attack every part of the defense.
Pistol is damn hard to make work if you want to be run first. I've been through that struggle a few times. If you're going to be pass first, it is pretty good but otherwise you can get in trouble pretty quickly.