What the heck is meant by "no fundamentals." To me the most critical fundamentals are pitching and hitting, over which the manager has only a slight effect--except, of course for how he manages the bullpen.
As for fielding, I think the only real sore spot has been 3B, over which Farrell has only so much control--for now, he is forced to use Sandoval. Besides, he's used, what 4 thirdbasemen so far? Bogaerts ain't great at SS, but no question he works really hard at it and out hits most other SS's. Moreland and Pedroia are fine if not gold glovers any more. The outfield is definitely above average. Leon has a positive DWAR at catcher, and Vazquez has a negative DWAR.
Baserunning, I agree, is suboptimal, but I blame some of that on Bill James and the overall Sox philosphy that bunting, stealing bases, etc are just not productive. Getting walks, however, is, so I have to ask you whether that's why you don't like the lack of fire?