Well everything you need is explained here:
http://wiki.maemo.org/Updating_the_tablet_firmware
It's in your own interest to read it well and don't start fiddling before you've understood it right.

Backup all your stuff from MyDocs (don't forget hidden directories) and make also a backup with the stock app. Double check you got everything.
Once you're safe that everything is secured, you flash the rootfs and then the emmc.
Your n900 comes out clean from this experience.
Then restore everything. When you restore from backup your application manager will offer you to re-download all your previous apps; you could exclude also some from the restore, especially bulky games, in order you're sure you don't clutter all your opt space again.

Good luck