1. Safety: Goldson was a big loss, and I expect them to replace him with the 31st or 34th overall selection. A good group of safeties will still be available there who are ready to start. They could also try to trade up for Vacarro with all the draft picks they have.
2. Defensive End: The 49ers defense was really hurt when Justin Smith went down with an injury late last season. He's getting up there in age, so they need a successor for him soon. They also need depth here. This is another position I expect them to address early. Two guys would fit perfectly for San Francisco: Dante Jones and Margus Hunt.
3. Cornerback: Rogers is getting old, Culliver was burned multiple times in the playoffs, and there isn't much depth behind him. San Francisco brought in Asomugha, who they may be able to revert back to form but he could also be completely done. I expect San Francisco to bring in a cornerback sometime in day two for some quality depth at least.
4. Nose Tackle: The 49ers lost Sopoaga to free agency, but they don't utilize the nose tackle position very much anyways. Glenn Dorsey may end up taking this role, but they'l also probably bring in a nose tackle in the middle rounds. There are a ton of NTs this year and only a select number of teams who need them, so they could find a starter with one of their third rounders.
5. Tight End: Walker has moved on to Tennessee, so they could use someone to take over that #2 tight end spot. They could find a decent one in the middle rounds, but they could also take a guy like Ertz early if he falls to them.
6. Depth: San Fransico has so many early picks and so few needs to fill. They will have the luxury of taking the best player available at any time, or taking big risk players who could pay off big. They can also take injured players such as Lattimore and let them sit for a season before trying to utilize them. San Francisco's front office will certainly have the most fun on draft day because there will be no pressure after the first few rounds.