Well....I have fixed some of the sorting problems. I did have "reversed normals" but it was done on purpose to create a cartoon like effect. That apparently is not going to work as anything in front of a reversed normal does not work.
At any rate, I got rid of the reversed normals and that fixed some problems, but I am still having problems with mdl polygon sorting. The entity/mdl object utilizes transparency and "concave" elements. I really am frustrated by this as trying to fix it is taking time away from other tasks. (I also tried "closing" all of the meshes.)
Also, is there any way to tag a model to not accept shadows. I would like to go for more of a cell-shaded look, so any mdl skin setup advice is appreciated.
Any other suggestions on fixing sorting issues is appreciated.