First of all, I still think the plan is likely Rex & Tyrod. But assuming that's off the table for this exercise:
1) Kyle Shanahan. He runs an offense predicated on the run game and it has worked very well. His offense led to a winning record in Cleveland with Hoyer at QB, and now look at Atlanta this year for how it works with more talent.
2) Ryan Mallett(UFA) or AJ McCarron (Trade), Brian Hoyer, Cardale Jones. Mallett is a big guy with a big arm who I believe Kyle could hide behind a superb play-action game, McCarron looked competent enough in limited action last year. Hoyer had success in Shanahan's offense in Cleveland with much less talent than we have, safe bet outside of injury risks. Cardale will be here developing, and on his short run to the national championship he thrived in an offense predicated on play action, a serious run threat, and big plays down the field.
3) Eric Berry would be a lovely acquisition.