I think I've found a way forward...
I was able to apply the armature modifier on the clothes.
Then, I delete all the shape keys on the model, I leave the particle modifier (I think is there because of the hair) and leave the mask modifier (which appears to be there for something to do with the shoes?), then apply the armature modifier only (in that stack of Armature/Mask/Particle).
I turned off autorun python scripts and also sent to render farm to test and both worked.
The only thing is I will have to do this for each model I render that has the IK settings (most all) and there is a LOT of shape keys to remove. I might be able to make a copy of the models and just remove the shape keys on all the models - I don't think I need them because I use the face panel to make expressions.
Thanks for all the suggestions and help!