I'd upgrade to 4.1 SP4, read the docs
on it and then perform an in-place knife edge upgrade.
You could stick with 4.1 SP3 if you wanted ... but this is a good opportunity to upgrade.
1) Document licenses / database location / BES Server Name (not windows host name, but rather the name of the BES Server in the BES Manager ... you need to make sure you make this the same as what it currently is)
2) Backup Server
3) Wipe Server
4) Install 2003 & Patches
5) Make sure you have 4.1 SP4 Full installation
6) Follow install guide for 4.1 SP4 install (print it out and go through all the checklists so you don't miss anything)
7) Smile at how easy that install was