Having some free time I went to look at film of the 9ers.
On defense they are very basic, they play P.Willis and N.Bowman free behind the line of scrimmage, their assignment is to read the play and react. They are not very strong towards the sides.
If you have a smart QB (we do) then reading what #52 and #53 do is the key to get yards against the defense.
Screens can be very effective if they attack the line or a total failure if they drop in coverage.
If Rodgers manages to read what those two linebackers will do then they will be defending with 9 players almost in every play.
A flea flicker can be a very good weapon because #52 and #53 react inmediately to running plays leaving the middle of the field totally empty.
On the offense I found something very curious. You need to have all the defenders standing, when defenders get to the ground Kapernick -I don't know exactly why- reacts calmly and executes good plays. If all the defenders are standing he usually seems confused and the play gets broken.
So don't get down!
Linebackers need to perform randomly to confuse Kapernick if they bite to the run or drop in coverage just too quickly he will promptly execute the antidote play, when the linebackers are in-between the play usually gets broken.
Kapernick is also very very effective against 3 rushers, I think we would need to rush 4 or 5 in every play.
This is a very difficult game but I was surprised to find that the defense of the 9ers is very simple, maybe that is why it is also very effective but against a smart QB it can be a problem. Andrew Luck and Drew Brees did very well against this defense.