since you're going to a seperate network (i.e. your users in the directory are not shared across these systems I assume) your only real option is to do a DiRT back up of your 3.1(3) system, reinstall from scratch pointing it to your Exchange 5.5 server in it's network and do a DiRT restore.
You can get information (including training video) and the latest version of DiRT from here:
http://www.ciscounitytools.com/App_DisasterRecoveryTools.htm