I was working on a project recently with 3D tracked footage and Plexus. I ran the Camera Tracker in AE and then created about 200 nulls from the track points. First of all, is this too many points? I've seen examples of Plexus in use and there seem to be more than this. I found that Plexus ran extremely sluggishly on my Mac Pro with this many nulls. What was weird to me is that, even when Null layers were turned off, Plexus still seemed to be trying to process them, but not actually rendering anything. I had it crash AE a couple times trying to render even at half res. It wasn't until I actually deleted some of the points that things sped up a bit. 100 seemed to be the max it could handle. I think at least if the layers are turned off, Plexus should ignore them and run faster. Here are my specs:
Please open a support ticket and submit the project file (just the .aep no footage). Also in the future please post your question in the corresponding product's discussion as it's likely to be missed if you start a new thread.