Morning! MSDE works on w2k3, problem with w2k3 and EXC55 is that the 55 Exchange System manager is not supported (it does work) on W2k3. If you are moving to EXC2k3 in a couple of months then could you wait for that before migrating?
Have you another SQL server? that would simplify - if you do, backup the db from MSDE and bring it back to the remote SQL server, then change the database in the console, now SQL is moved. Install BES3.6.4 on new W2K3 server using same mailbox and pointing to remote SQL instance, stop services on old BES and start on new - if necessary backup DB again and add to MSDE on new BES.
Hope this helps