As good as Henderson has been overall, I think he kind of contributes to that inability to sustain long drives. As much of a nose as he has for long touchdown runs, they can come at the cost of a few -1 or zero yardage runs where he's slow-playing his cut rather than just sticking his foot in the ground and moving forward. Some improvement from him in that could help with drives stalling out from unfavorable down and distance.
Overall on the running game though, the OL could use some further improvements. Hopefully Wilson improves in year 2 and Bradbury is upgraded either at C or LG with Wilson kicking over to center. Onwenu and Moses could be upgraded, but how practical it is to do so might depend on free agent costs and the draft board.
Another indirect issue for the running game is the lack of separation from the WRs. As productive as our downfield passing game has been, it doesn't very much from WR separation so teams are more than content to play one on one and allocate extra players to the box to play the run and blitz. Continued improvement from Boutte, Diggs being in year 2 back from injury and possibly upgrading Hollins from outside the organization and/or KWilliams becoming a factor are all things that could help. We have a productive passing game now but it's mostly against favorable defenses. It'd be nice to see continued progress to where it can maintain that production while also forcing defenses to leave the run game open more to defend it.