Thanks for the post.
a couple of things...
The OL not opening up any holes, and the Niners LB's are untouched, unblocked too often.
Bilal Powell must play more on 1st/2nd downs, and Sparano must call for more runs outside the Tackles with him. Defense is clogging the middle with no outside threat.
Kerley is very good, and might be an upgrade in place of Tone.
Mark and the O miss Keller more than I thought.