They have to clean house on D. Guys like Chancellor, Avril, and Sherman can't be counted on after their injuries. They were reportedly trying to trade Sherman the last 2 years because of his contract, so I bet they cut him this offseason. Their backups have played pretty well this year, and are cheap. Even without investing a ton of draft capital, they could still have a top 10 D with Wagner, Wright, and Thomas as their core.
Their O though, is a problem. I think they tried to address the running game this year when they signed Eddie Lacy, but he's been a bust for them. They were most successful when Lynch was running over people for them - their OLine has never been great under Carroll. I would definitely go RB early if I were them, especially with the Rams' run defense as inconsistent as it is.
I would also invest in a mobile backup QB. It's a miracle Russell Wilson hasn't missed a game - I think he's hidden a number of injuries over the years, he's that much of a competitor. There was a time when Kaepernick looked pretty durable, and then he ended up on IR with like 4 different injuries.
