This might save you some time & frustration. Get yourself a black Endura/Delica clip. You might be able to get it direct from Spyderco or, if not, there's at least one or two available on a 'certain popular auction site' (that pretty much everyone knows about). If you search for 'Endura clip', you'll see 'em. They are available in both stainless and black finish.
I just finished comparing my Manix 2 clip with my Endura's. The Endura clip has a hole drilled through it (so it fits over the lanyard hole on the Endura), but the screw holes are spaced in the same dimensions as on the Manix 2. Also, the Manix 2's clip screws are bigger diameter than the Endura's, but they'll still fit through the screw holes on the Endura's clip (I swapped clips on mine just to be sure). So make sure you retain the Manix 2's screws to make the swap. The only downside, I suppose, is that the screws themselves are not black (on either model), but you might even be able to find some elsewhere, if it's that big a deal for you.