Mesh ID

Chunck will probably know, but one thing that everyone always advices, and works like a charm, is to start over from scratch. You'll most likely see where you made a mistake and the process will feel much simpler the second time around and it will solidify the knowledge in your mind. 

Sorry for the late reply! The first thing I'd want to check is to make sure that the Mesh ID texture is actually slotted into the Material Section. If you take a look in InstaMAT, is your baked texture added into the appropriate slot?

You could start from scratch scratch and remodel everything yes, or you could also start watching the course from the start to see if you missed a step and hope along where you left and skip the modeling part, since your model doesn't have any issues.

Hmmm, alright well it looks like a texture is slotted in that channel, however it looks like it and a couple other texture maps did not bake properly. For some of the other maps like the Ambient Occlusion, does it appear to have baked correctly? (You can check what it looks like on your model by pressing the "C" key and cycling through the baked textures).

The first thing I'll recommend if you haven't tried it already: Create a new InstaMAT project and try baking again. This could be an easy solution that may fix things without us having to get too deep into troubleshooting.

If you give that a go and things still are not working:

1. Make sure that your high and low-poly models are in the same exact position when exporting from Blender
2. Double check that both the models have their normals facing the correct way (we don't want faces with inverted normals / backfaces showing)
   
3. Make sure that you have both the High-poly and Low-poly models loaded into InstaMAT when you are in the baking panel
4. Double check that the High-poly model file isn't empty (I've done that a couple times...)
5. In InstaMAT, play around with the ray settings to see if you need a greater ray distance

Like Omar had mentioned, it may be beneficial to retrace some of your steps leading up to this point in the series. Texture Baking is often a mistake that happened several steps prior, so it could very well be an issue that exists outside of InstaMAT. Give some of those ideas a try and I'll be happy to continue troubleshooting with you if that doesn't work! :)