I have done all of my testing and setup of JMS2WIN thus far on a server using Apache 2 Handler. We are now wanting to switch to suPHP for security reasons before launch. Are there any things that I need to change or be aware of that may be affected in regards to the functionality of JMS2WIN because of this change?

Thanks again!

I recommend sometime suPHP because it simplify the permission issues.
If you change of server of setting, there is only few things that must be checked in terms of permission.

if the suhosin apache module is installed, you will not be able to have shared sessions (single sign-in)
If you have "open_basedir" defined, this could lead to permission problem when deploying a slave site outside the "open_basedir"

The advantage of suPHP is that it uses the same owner/group than the script that is executed. This avoid plenty of problem between a owner XXX and owner apaches or nobody.