The 4-3 / 3-4 ought to be sufficient to stop outside runs, and putting more players with poor tackling ratings on the field doesn't seem like the correct approach to me (unless your team happens to have a stable of strong tackling CBs, which I doubt).
I'd look first as to what plays you are calling when you suspect the offense is going to run the football. Calling a Cover 1 or Cover 3, for example, will align your defense pre-snap in a single-high safety look. By the nature of the strong safety being closer to the line of scrimmage, this coverage has a natural strength in run defense. If you are routinely calling Cover 2, that eighth man isn't going to line up in the box by default, putting tremendous strain on your linebackers to make every play. This is fine if you have great LBs, but most teams can't match the 49ers to this end. If you are routinely calling 2 Man coverage, the perimeter players by default are going to turn and run with receivers, and as such they aren't even looking for a run play and that will hurt one's run support; combine that with two high safeties both stepping backwards by default and you get a play I don't like against the run very much.
I'd recommend taking a hard look at your playcalling before you start trying out more exotic "labbed" packages. The biggest thing I've learned about defense this year is that there has to be a known purpose to what one is calling, because on a single given play, a defense can't cover everything, and they must rather look and try to take away what it thinks the offense wants to do the most often and force the offense out of its comfort zone.