That's probably because freedom of speech and freedom from unlawful search are perceived as rights that can wax and wane, but can always be restored.

The loss of the right to bare arms is perceived as an end-game. Once disarmed, there's no going back.

In all fairness, all the other Bill of Rights amendments were already applied to the states.

The ACLU pretty regularly takes 4th and 5th Amendment cases.

By recent win, are you talking about McDonald v. Chicago? That's actually Alan Gura and the Second Amendment Foundation. They're also responsible for Heller v. DC, which the NRA tried to interfere with. In fact, most of the recent 2nd amendment successes have been Gura's work, not the NRA's.

The NRA is pro-hunting instead of being pro-second-amendment. Sometimes the two interests intersect, but not always.

The NRA has the advantage that it is aligned with the interests of a major domestic industry and everyone who works in it. The ACLU and EFF don't really have that kind of alignment, which one would assume makes it harder to raise funds, etc.

The NRA only protects hunter's rights (sometimes at the expense of non-hunting gun owners). The most recent victories in the supreme court were by the Second Amendment Foundation, and think-tanks like the Cato institute have done much more for the second amendment than the NRA.

While the last decade or so has been good for supporter of gun rights, the entire 20th century was not. A lot of what gun rights activists are trying to do now is gain back some of the rights they lost in the 20th century.

As a side note, I think it is interesting is that 3D printer and other consumer-level CAD technology may be for the Second Amendment what the internet was for the First: a way to bypass government regulations altogether.

Please do not mistake my post for an endorsement of pro- or anti-gun viewpoints, I just want to clarify that the NRA isn't actually all that great for gun rights, and gun rights activists haven't been all that successful until recently.