The niners currently have 38 players signed for the 2014 season. This includes Alex Smith, 12 marginal low- salary players (Mostly 2012 late-round draft picks, FAs and future contracts). The account for around $80 million of cap space. The 24 quality players, from Carlos Rogers to Bruce Miller, occupy a salary cap of $82.4M.
I estimate the 2013-14 draft classes to take up $10.5M of cap space for 14 players. This leaves 15 minimum-wage players ($7.5M) to fill up the 53-spot roster.If the salary cap hovers around $124M in 2014, the cap room for FA salaries and extensions is $24M.
There are five key players that needs to be extended at market prices. Unfortunately, four of them deserved top-5 money for their position, even taking team discounts into consideration. For the sake of argument, extend all of them 4 years, until 2018.
Mike Iupati, assuming he is paid $7.5M in 2015-18, extended this year would get $6M/year average. Anthony Davis could also get a similar deal (6M/year). Michael Crabtree, assuming a $10M/year extension, a 6-year deal would come to $8.5M/year. Their extension later this year should eat up all available cap space left after the 2013 training camp.
Aldon Smith had the least leverage. He is eligible for a 5th-year extension at transition player tag (now $8.2M for linebackers) in 2015, then could be franchised in 2016. If he is getting $11M in 2017-18, his contract comes to $8.5M/year.
Giving Colin Kaepernick a 20-million/year deal in this 4-year period, would result in $16M/year for 5 years.
This adds up to a staggering 45 million cap hit from the new contracts. This is an increase of 27 million from current 2014 cap hit of $17.7M. Their current contracts would add another $4.6M from signing bonus proration. Make it a $31M increase overall . Higher than the $24M space available, but would require only a moderate backloading of these contracts to work. Further backloading can make room for limited additional FA signings.
Other possible cuts
I did not include the possiblility of cutting Carlos Rogers would save $5.1M cap space in 2014, the majority of the pay of an impact FA signing. Some further restructuring or cuts are also possible depending on performance (Gore). Cuts this year (Akers, Whitner) could make further wiggle room in 2014.
TL;DR: The niners seems to have cap room to extend Iupati, A. Davis, Crabtree, Aldon and Kaepernick, have some wiggle room to sign one big-money free agent, and extend a few other players (Walker, Culliver, Brown, Hunter, UDFAs).