So here it goes. For simplicity, I assume everyone (except Lattimore and Marquard) gets healty for the start of the season. Assumed starters are in bold.
QB (3): Kaepernick, McCoy, Tolzien
Tolzien: he seems to be scared of losing his roster spot, but Daniels has a long way to go
RB (5): Gore, Hunter, James, Dixon, Miller
Dixon: The team signed enough good ST players as his presence might be superfluous, but he is the only short-yardage back on the team.
Miller: He is only a blocking FB (even if a very good one) and an ST player. Dixon, if improves in blocking, might beat him out, being more versatile (also valid run threat unlike Miller, and can catch screen passes as well)
TE (3): Davis, MacDonald, Celek
Celek: he seemed to solidify his position, as the team was willing to cut Morrah
WR (6): Boldin, Manningham, Jenkins, Williams, Patton, Lockette
Lockette is in battle with every other receiver on the roster
OT(2): Staley, Davis
OG(4): Iupati, Boone, Snyder, Looney
C(2): Goodwin, Kilgore
Kilgore, Looney: I take not drafting a guard or center as a sign they are doing OK
Snyder: He got a lot of money guaranteed, the guy who might beat him out is Wiggins
DT (2): Dorsey, Williams
DE (5): Smith, MacDonald, Dobbs, Dial, Carradine
Dial: as a 5th-round draft pick, the roster spot is his to lose (like Slowey managed to do last year)
Dobbs: he is the guy who can play backup week 1, I see no one else on the roster for that spot
Carradine: if he starts on the PUP, his spot is taken by a LB as placeholder
OLB(4): Smith, Brooks, Haralson, Lemonier
ILB (4): Willis, Bowman, Skuta, Moody
Moody, Skuta: the team would not have signed a FA special teamer, and drafted another one, if they would be satisfied with Wilhoite. Fleming will be put on the PS to see what he can do. Cam Johnson probably makes the PS
S(5): Whitner, Reid, Dahl, McBath, Spillman
Spillman: He might be the odd man out. He was not as good on ST as Baalke thought he would be signing him for 3 years. Then another ST player (Dahl) was signed. The primary FS backup was McBath last year. We know nothing about Robinson.
Whitner: I don't think his roster spot is guaranteed. He was just that bad last year, both in coverage and run support. If he was the playcaller for the defensive backfield, he should get his share of blame, too. If Whitner is out, I foresee a Reid and McBath/Dahl as the starting safeties.
CB(5): Brown, Rogers, Awesomeguy, Culliver, Cox
If Awesomeguy makes the team, the 4 "starter" corners would see the playing field based on matchups. Cox is in for Dime and the occasional nickel packages. Brock is cut. None of the rookie CBs stood out positively in the mincamp.
Special teams (3)
Dawson, Lee, McDermott
Only the 49ers have 3 long snappers in the NFL- despite having only two kickers. They would not do it unless they were seriously considering to replace Jennings. My guess is that McDermott is the main candidate, Jennings is the fallback option and Kyle Nelson is a "proven veteran" brought in to push both.
Practice Squad (8)
ILB Fleming/Stupar (they need one extra ILB)
Crabtree, Marquardt, Lattimore, Debniak, Carswell
It would be the 3rd year Wiggins would spend on the PS, so expect him to be shuffled a lot like it happened to Hall last year. It should be noted that the team will keep at least 10 OLmen on roster and the PS, enough for the 1st and scout teams.