Upgrading from Windows Vista to Windows 7 (custom installation).
This also may help you, for custom installation.
Custom install mentioned here is doing installation without formatting HDD. Hope it wont help you.
For Doing a Clean install, you have to boot from the Upgrade DVD and install.
You can boot from a upgrade media, since both upgrade and full installation disks are same but the product keys only will vary.
For these clarifications, Check the Paul Thurrott's Supersite link, I mentioned in previous reply. It'll give you a step by step clean installation of Win 7 using upgrade media and Product activation.
Please do Format, to avoid errors, and Please do back up all your data before trying Clean install.
P.S: If you are doing a Clean Install, wiping HDD, get ready to install all applications once again. It may pain a bit, but you will get an error free system