Za941 When I loaded your file initially, I walked back up through the output in the script editor - right at the top of the output, there were one or two muscles that presented errors, so I first removed them from the solver.
When I did this, the solver was then able to compute again.
I think that in some of those cases, the source of the issue was that the display mode for the muscle was set to "3", which effectively changed the number of vertices given to the embedder for the muscle mesh to deform, which no longer matched the number of vertices stored when the muscle was first instantiated.
This could be the cause of the "list index out of range" error.
After I got the solver working again, I then selected the solver node and copied the settings using the "Ziva Transfer->copy" option.
I then removed all of the ziva nodes from the scene using the following lines of python:
import zBuilder.zMaya as mz
I then made sure that all meshes we set to a display mode of "0", selected all of the muscles and ran the "Ziva Tools-> Run Mesh Analysis" function and corrected all of the issues with the muscle geometry (there were only a few small issues - some of the muscles were inverted and some had some self intersections)
After making those corrections, I selected all of the muscles, and rand the following line of MEL:
deformer -type "tweak";
And then deleted history on the muscles.
(This was to ensure that there were no component level tweaks on the muscle meshes)
I then selected all of the bone geometry and added them as bones.
I selected all of the muscle geometry and added them as muscles
then selected the muscles and ran "Ziva Transfer->paste" to bring back the rigging I copied at the beginning.
I hope this helps!