You shouldn't have to do a backup because you are already backing up right?!?!??! Always have backups.
That said...
The odds of truly losing your data are almost non-existent. At worst you'll have a botched install and maybe a Stop 0x000007B at boot or something. Your data will be fine and a parallel install would retrieve everything.
Some things you can do ahead of time that will increase your chances of a good repair:
1. Get rid of all startup items. Use MSConfig to clear out startup items and all non-ms services.
2. Uninstall anything that uses filter drivers. This includes CD burning software, some 3rd party backup utilities and antivirus.
3. Get rid of any utilities that monitor your hardware.
A repair will basically redectect hardware and perform a clean install. it leaves any 3rd party registry entries so all your programs will be intact. It will not alter anything in your documents and settings, programs or basically anything on your drive outside the Windows folder.
The only thing that can really put you in trouble is some third party service or driver set to boot that fails to run on your new hardware. Being 3rd party the registry entries and startup sequence will be preserved. If it fails the computer won't boot and it's 10x a pain in the ass to get that fixed...requires a parallel install usually to get to the registry.