If you don't need to analyse the forces in the upper-body, then it is a good idea to exclude it from the analysis. You should really also remove the markers from the trunk and head segment, and just add the reaction force on all degrees of freedom above the pelvis.
See this post:
That should simplify your model even more.
Well first simplify your model as wrote above. That should make the model more robust. THen you can also try to improve the initial guess of the marker positions. That some times also helps.
Yes. That could also help. Marker drop-outs are not good when there are only a few markers per segment.
That should be enough in most cases. You can consider to manually adjust the strength index of the model. In the default model, strength is scaled with the hight and weight of the model, but that is not always a good assumption.
Best wishes,
Morten