Just some friendly advice - forget about using WM (Windows Messenger)
for your application. Its not really 'free' if you plan to use any
feature besides voice.
In SIP mode, IM (and I'll bet WB (whiteboard) has the similar
issues) expects a header that contains a key
generated by LCS. I dont know of anyone
who has managed to 'crack' this and use SER as an IM/WB proxy for WM
for free.
If you must use WM, then LCS is your only real option for fully
functioning system - and that will cost you per seat for Microsoft.
They might have some education discounts or freebies but setup of what
you want will still require someone to host it and/or consulting fees
for setup. Any you will still have firewall issues unless all remote
users have a uPnP router.
Another approach for you it to use the sipc system. It free for
educational and research and I bet it work with SER (but haven't tried
myself).
http://www1.cs.columbia.edu/~xiaotaow/sipc/
Mark