My advice is to play your game. All of what you listed can be stopped.
1-3 Bring a safety into the box. When I play a dominant run game I bring my run stopping strong safety into the box. It work wonders and it is sim. Why do some think that you can stop a great running game with only 6 and 7 players in the box and many times thay dont even have a run stopping d linemen/linbacker. Not your fault if they want to use all their legends on defensive backs.
4-6 Is just sour apples. There are tons of coverages (zone, man, and hybrid) that can manage short, long, and whatever.
7, See 1-3
8, block better, slide protection, keep backs in, hot route to vacant space
9, Cover 2 press, Cover 3 weak and hot route your olb to the flat, etc
10, play a cover 3 and hot route a lb to man up on him
11, see Tom Landry, Martz etc formation shifts is one of the most under ultilize aspect in this game. . I play zone to keep my assignments the same.
I played you before and I like your game. I like seeing new wrinkles. I was called cheese because I was running too many 4 and 5 wr sets. Like I said before play your game.
Peace