I think the thing we have to look at with Tolzien and Kaep is that Tolzien looks better now but the ceiling is not that high. Whereas Kaep is still very raw and has a much higher cieling...if developed correctly and given enough time, Kaep is expected to develop into a much better QB then Tolzien. I like them both, I think whoever we end up keeping, Niners are deep at QB.
My guess is, it will be Smith, Kaep, Johnson...however, say Smith is to go down early in the season, Johnson will probably start over Kaep just because he has some experience and is more NFL ready.