1. It depends on your perspective. If the first scenario is looked at from the positive z direction and looking down at the origin, then let's agree to always keep that orientation when we give our final conclusion for the direction of precession. With this orientation the precession is counterclockwise when the angular momentum is positive.
When you look at the one with negative angular momentum it precesses in the counter clockwise direction while looking from above, too.
Why? Consider the first scenario where the angular momentum points at you (more or less) in the positive z direction but now let's flip the B field. The precession changes to clockwise because of the opposite direction of the B field. But this situation (spin up, B down, +z viewing point) is identical to you looking from the bottom toward the origin in the initial configuration (spin down, B up, -z viewing point) - i.e. in this configuration the vector precesses clockwise to the observer. But if we switch back to our initial viewing point, the positive z, and leave the B and spin alone, the precession will be counterclockwise from our viewing point.
The logical progression would be this:
(proton, spin up, B up, +z viewing point) - counterclockwise
(proton, spin up, B down, +z viewing point) - clockwise
(proton, spin down, B up, -z viewing point) - clockwise
(proton, spin down, B up, +z viewing point) - counterclockwise
If you change to an electron the precession will be opposite in all situations to that of the proton.
You can see that changing the angular momentum doesn't change the precession. But changing B, your perspective, or the sign of the charge does change the perceived precession.2. If you look at the torque on a proton you will see that the resultant precession is the same as above, counterclockwise. All protons precess in the counterclockwise direction when viewed from above if the B field is pointing at you.If you would like an intuitive mind model for figuring out the torques due to angular momentum, check out this excerpt from an old physics book.
http://img53.imageshack.us/img53/7207/angularmomenscan2xj4.jpg