John,
you should also consider budgeting in some hours from Wolfram services. WSM and Mathematica are so powerful that they have considerable learning curves. It is hard to know "best practices" without using both together. Most things can be done in either program but there is often a best way to do it. A few hours with someone who can help you get your problem launched in the right direction goes a long way. (For example, if you want to do animations later on it is best to start out with that in mind).
Additionally, I have found the support on the SystemModeler forum (in this community) is very strong and usually quicker than the premium support.
I would be interested in what you ultimately pick. If you want to talk to an actual user (who also uses MATLAB, SIMULINK and others), Please feel free to contact me outside of this forum.
Regards