The 'auction site' frequently has a few clips listed for the Endura, in black or polished. The Endura clips will fit the Manix 2. I have both, and I verified this a while back when somebody else asked this question. The Endura clip also has a hole through it, because it's mounted directly over the lanyard hole on the Endura, but the holes for the screws are laid out in the same pattern as for the Manix 2. If I remember correctly, the screws to mount the clip on the Manix 2 are larger. Just make sure to keep the same screws if you swap a clip from an Endura (for which the clip screws are a bit smaller).
I'm pretty sure you can order a black Endura clip from Spyderco, if all else fails.