TL;DR: Baalke and Maraathe will have to clear over $3M cap space
Currently the team is under the cap limit, due to the top-51 rule. I took a look at how the cap situation would look at at the start of the season. I used the salaries as listed by Jason Hurley at ninercaphell.com, with rookie salary projection originally by overthecap.com.
I assumed a roster projection that was more or less conservative, keeping players from 2012 if possible instead of cheaper rookies.I have Brock not making the team due to his high salary. Two players will start the season on the IR (Manningham and Lattimore), but their salary counts in the cap. I assumed the Practice Squad players would be paid $6000 for a game (it was $5700/game in 2012). I do not count the signing bonus/guarantees paid to the UDFAs.
The 53+2 guys on the roster/PUP would account for $124.687M.
The 8 practice squad players account for $768K.
The dead money is $973K.
This gives a total cap expenditure of $126.428M.
Available cap space (again, according to ninercaphell.com) is $126.277M.
So the 49ers are projected to be $151k over the salary cap.
Some additional space must also be made. One or two guys who would make the roster will get injured in the training camp, and will have to be put on PUP/IR, and a rookie or vet must be signed to play in his place. Baalke might decide to pay rookie minimum to a PS player who he really wants to keep from getting poached. Then at least another $1M for emergency signings late in the season.
So at least $3M space must be made. One option is replacing fringe veterans paid over $1M by rookies, but the only candidate for this is Spillman. If Assomugha is cut, Brock stays. Second option is to restructure/extend current starters (JSmith, Brown, Gore), which must be done unless the team decides to cut current starters.