Near tool and Model Builder

[gis_novice]

I'm currently working on creating a model that will select the name of a species in one point shapefile, the name of the same species in another point shapefile, and then perform a near analysis to get a distance from one point to another, and do this until all of the species have been selected. I figured the Near tool would work okay for this, and on a test run it did work just fine. (I attempted to use the Point Distance tool as well, but had no way to clear my selection with that for some reason.)

However, now the Near tool seems to be broken. ArcMap generates a 9999 error and says the near fuction could not be executed. So I closed and restarted my project. Nothing. I then restarted my computer. Still nothing. I then  recreated the model again and tried to run it, but it still gave me the same error. I can't find anything pertinent on ESRI's support site (how can anyone, now?), so I thought I would try here. Does anyone have any ideas why this would suddenly stop working and what I could possible do to get it working again? I'm quite new to Model Builder (and the Near tool, actually), so I'm wondering if it could just be human error. Thanks in advance!