Re Roman's play calling, etc.: first, I agree that when we lose we have gotten away from the running game. But we have not gone away from the running game in the Kaepernick era completely.
Chicago: 29 rush (121 yards), 23 passes.
New Orleans: 31 (144 yards) , 25 passes).
Miami, 28 rush (155 yards), 23 pass.
Against NE, we rushed 39 times (180 yards) to 25 passes.

But in the Rams loss: 36 (148 yards), 32 passes.
Seattle: 19 (82 yards), 36 pass.

This is a similar pattern as with Alex. For example:
Green Bay: 32 rush (186), 26 pass.
Detroit: 27 (148), 31 pass.
But against:
Giants: 17 rush (80 yards), 37 pass.
Vikings: 20 rush (89 yards), 35 pass.

So it isn't that we are rushing less with Kap; it's that we are giving up on the run in our losses. In all of our losses we rushed for over 4 yards per carry, but in the 3 losses when we got dominated, we gave up on the run very quickly.

The pistol works with the run well because the running back lines up behind the quarterback. It also allows for the read option. And Frank has always run well on draws and delays. (And he is in general getting about the same number of carries as under Alex.) But we are throwing longer passes, and it seems to me we are throwing more earlier.

So I am not crazy about some of Roman's play calling. But it isn't so much how we run but when we run that I am not crazy about.