I fixed the weird glitches that happened on the Optimization branch yesterday. (I also upgraded the project to Unity 2018.2 and reorganized the scripts a little bit). It's all merged into the master branch at the moment, if you're still interested. Thanks again for confirming the TextMesh instructions, they worked for me as well.
The problem was that I had forgotten to also reset the MuscleJoint rigidbodies when resetting the bones, which caused them to disconnect and glitch out.
I'm now working on the next big release with tons of new features that I'm very excited about.