Updated for recent FA moves (Haralson, Dawson, Moore)
My take on the current roster situation, as the roster holes keep filling up. I tried to fill the 53-player roster from the players already under contract, with roster locks and those on the "strong bubble" (italicized). I see 31 positions that are "locked" with an established starter or key backup player. Another 14 players are on the "strong bubble" - solid backups but without guaranteed spots. 5 positional needs are currently not filled. Three more roster sports are available beyond the primary positional needs. The cap casualty candidates were considered 'locks' at this point, they are unlikely to be cut unless their replacement is available.
The last category is the weak bubble. I put several players here that were on the roster during 2012, but hardly were active if at all (Hampton, TJE, Johnson, Robinson). They will battle veteran FAs, late-round draft picks and UDFAs for backup positions.
Offense: 14 lock, 6 bubble, 3 not filled
Running Back (4-1): Miller, Gore, James, Hunter - Dixon
Quarterback(1-1): Kaeperick - Tolzien
Wide Receiver(3-1): Crabtree, Boldin, Jenkins - Williams
Tight End (1-1): V. Davis - Celek
Offensive Line (5-2): Staley, Iupati, Goodwin, Boone, A. Davis - Kilgore, Looney
Unfilled needs are QB2/3, TE2/3 and OT3. The team is set at WR and RB positions. Manningham is expected to be put on the PUP list, so he is not listed here. The team has no #2 QB at the moment, although Tolzien will get his chance to fight for the spot. Celek spot seems to be secure unless we draft 2 TEs (which might happen). A swing tackle would improve the OLine backup considerably, so the team won't have to replace Boone if Staley or A. Davis is injured. It would also be a future insurance if either tackles cannot be extended. I expect two of the three leftover roster spot to be on the offensive side (RB6/WR5/WR6/TE4/OL9).
Defense: 14 lock, 8 bubble, 2 not filled
Defensive Line (4-2): Smith, McDonald, Dorsey, Williams - Dobbs, Tukuafu
Outside Linebacker (2-2): Brooks, Smith - Haralson, one of Fleming or Johnson
Inside Linebacker: (2-2): Willis, Bowman - Wilhoite, Skuta
Safety (2-1): Whitner, Dahl - Spillman
Corner (4-1): Rogers, Brown, Culliver, Brock - Cox
Unfilled needs are DL3 and S1. The Defensive Line has the two starter DEs. Either get a stud NT that can pass rush, or someone to spell Smith/McDonald, or both. Williams and Dorsey can battle for the NT position if necessary, and both are capable to sub at DE or nickel DT. Dobbs was used mostly as DE in both 3-4 and nickel. Tukuafu was mainly used as the jumbo Fullback. If we draft both an NT and a DE, Dobbs or Tukuafu won't make the roster.
The ILB position appears to be set, Skuta is paid as a backup not an ST-only player. Haralson apparently secured his position as the primary OLB backup by agreeing to a paycut, but his spot can be in danger in the training camp. Johnson and Fleming will battle it out for the other backup spot. The secondary might be before a major upheaval. Everyone except Brown and Culliver could be cut before the draft or after the training camp, due to preformance/salary reasons. The Dahl signing seems to be for depth and ST play, but it puts Spillman position on the line. One more roster spot is up for grabs for the most talented player left over.
Special teams (3)
LS Jennings, P Lee, K Dawson
Placekicker need is filled, but I can see the team draft someone in the 7th round and put him on the PS. The core of the coverage teams remains, with minimal turnover, which bodes well for the next season. There are kick/punt returners on the roster, even if we don't get any new player for the position.
Weak Bubble and camp bodies
WR Hall, Lockette, Hastings, Moore
OL Wiggins, Netter, Tribue
DL Jerod-Eddie, Divens
OLB Johnson, Fleming, Stupar
S Thomas, Robinson
We have no idea how the FO and the coaches regard there players. All the four WRs appeared in an NFL game, they are all fringe players, and only Lockette provides something unique (size, speed and deep threat). Hampton got a roster spot. Some have good opinion on Wiggins. Fleming was a 4th round pick but got injured on the first day of the minicamp - so threat him as a new 4th-round draft pick. Johnson and TJE made the roster at the end of the season. Robinson made the team while Thomas did not, so I have to guess he is the better prospect.
Of these players, the following have realistic shot to make the roster:
Johnson and Fleming battle it out for OLB4
Hampton for RB6
Lockette for WR5
Johnson and Fleming for DE4
Robinson for S4.
Jerod-Eddie to replace Dobbs or Tukuafu.
To summarize, the must-fill positions in the draft are S1, DE3, TE2/3, QB2/3 and OT3. Of these, I'd predict S1 and DE3 as two of our top-3 draft choices, the others can be filled later. These account for 5 total draft picks. This leaves three flexible roster spots available for new picks or fringe players on the roster. A few positions that are not a primary need, but can be improved if a talented player falls in the draft are RB, WR, TE, OLB, NT, CB and S.
The 49ers have 14 draft picks total. The two 7th-rounder compensatory picks cannot be traded, these picks will battle for the practice squad. This leaves 12 picks left to fill at least 5 but no more than 8 roster spots, so 4-7 picks are available to trade up or into 2014.