MeshMixer is the program that I used to fix and combine my Catch with stock 3D models. Although the website looks like it was designed by a cross-eyed monkey, MeshMixer is a pretty sophisticated piece of software. It uses an obscene amount of your CPU while running, so make sure you save often (to avoid losing everything in case of a crash) and close any other programs you have open before starting.
Consider this step just a basic overview of MeshMixer. My goal with this program was to take two models, my face and a stock model I found online, and merge the meshes into a single model. Essentially, I wanted to slap my face on a body. If you have your own program that can merge two models I recommend you use it, as MeshMixer can be quite fiddly.
Cross your fingers and open MeshMixer.
Go to File > Import and select your repaired OBJ file. It's possible to import your original unrepaired OBJ, but you'll be unable to select invalid surfaces, which makes it pretty much useless.
Just a quick tip to save you the frustration I faced. Rotate your view by holding Alt+Left Mouse Button, Pan with Alt+Shift+Left Mouse Button, and Zoom with Alt+Right Mouse Button. If you're more familiar with 3D editing software you may have already known this, but I'm not, so I didn't, and it made me want to put my fist through my monitor.
Use the Select Tool (S) to color in the parts of your face that you want to work with. Hold Shift to deselect areas, and hold the Right Mouse Button while moving up and down to grow or shrink your selected area. If you start clicking in the space outside your model you will automatically switch to the lasso tool. I've found this to be the most useful way to select areas of the model, but be careful. You have control over your relative X and Y axes while lassoing, but your Z axis has infinite depth. What this means is that if you lasso a small circle around your nose you will also end up selecting a small circle on the back of your head. Mesh mixer will select everything inside that circle, even if it's on the other side of the model. Sometimes when you try to select something with the lasso it will accidently select everything except the lassoed area. If this happens just click Modify Selection > Inverse (I) to switch it to the correct selection.
One you have the area you want to edit selected you have a couple basic tools available. Edit > Discard (X) will simply delete your highlighted areas, often making you model non-watertight again (don't worry, you can always fix it again in NetFabb). This is the simplest way to remove unwanted sections of your model. Edit > Erase and Fill (F) will attempt to delete your selection and fill in the gap. It often fails at this, but it's a simple way to try to smooth out flaring and intersections caused by combining your models.
Deformations > Transform Faces (T) will be your bread and butter. This is the only way I've found to actually move, rotate, and scale the models in MeshMixer. The best way to move your whole model is to click the Select Tool and press Ctrl+ A to highlight everything. This ensures that you don't miss any surfaces that may be hiding somewhere. One you've highlighted your selection and clicked Transform Faces you should be able to move your selected area around.
If you try to import another model MeshMixer will ask you if you want to Replace or Append the current mesh. Unless you're starting over you should always append. You can switch between which model you want to work on when you don't have a tool selected; when using the Select Tool you will only be able to select surfaces on the model with which you are currently working.
If you want to learn more about MeshMixer you can find their tutorials page here.
Now that you have a basic idea of how MeshMixer works, I'll walk you through mashing up two different models.