given that our defense is one of the best in the NFL in the red-zone, I would have thought that we could have stopped them twice and force the FG with around 3.15-3.20 left to go. Given that we had already forced 11 third downs and allowed just 4 conversions - 2 of which were on 3rd and 1, I would have felt confident in getting the ball back.
We should never have lost the 3rd and 7 that Kaepernick converted - they were never ever going to risk an incompletion and stopping the clock, so all should have been keyed in on stopping Kaepernick once he didn't hand off.
That is far more important than calling timeouts too early. That said, I would have have called the first one on third down, as a 2nd down conversion would have still allowed the Niners to run off the clock past the 2 minute warning, and even if they didn't convert, but left themselves with a 3rd and short, you'd be thinking - worst case scenario we have to use two timeouts when they convert their third and short, but at least that leaves us with over a minute with the ball, but if they fail to convert, we can stop the clock for the FG and then have a timeout to use when we try and drive back up the field, so don't have to worry about throwing to the sidelines.
The thing that most annoyed me was that the Niners were able to run down 39 seconds of clock before the 2 minute warning gave them a free timeout breath