Welcome to Seven Forums.
Don't know how your going to get the Vaio pre-installed programs.
Someone here with a Vaio might be able to tell you that.
When you installed the first time did you activate the Windows 7?
You can use the Seven Forums tutorial Clean Install with a Upgrade Windows 7 Version
, since you have a previous version Windows, if they ever ask.
For reference: Clean Installation with Windows 7
If you have activated the 32bit install, MS might allow the 64bit Windows 7 to be activated or you might have to get their permission. Just explain that you want the 64bit Windows 7 and have formatted over the 32bit version. Won't be a problem.
When you install the 64bit Windows 7 just select the partition you want to install on and it won't touch your Data partition.
Always backup your HD before you start any installation just in case you need to restore it.
Let us know if you have any more questions.