Install clean version of Leopard on external, then use as internal

I need a bigger drive for my MacBook pro, so I bought a 320 GB 2.5" drive and an enclosure. I am in the middle of installing 10.5 on the external. Here's what I want to do:
1) Create a new user "stuart" on the external (same name as my current user on my internal), but don't copy anything from internal yet
2) Install clean versions of all my current apps
3) Then bring over my documents, but not all the accumulated cruft.
What I'm trying to avoid is bringing over all the cruft that's presumably accumulated in my Library folder and elsewhere. I just want clean apps and my user documents.
So my questions are: If I create "stuart" when installing, then if I later use Migration Assistant to move my documents, does MA insist on creating another user, or will it be happy to move all my documents from my current user folder, also called "stuart", to the new user folder?
Also, will MA automatically move all the old stuff from my Library folder?
Finally, if I manually move my files over, will there be potential permissions problems? Is the mere fact that both users are called "stuart" mean that the permissions will carry over fine?

You cannot use MA to move only your documents. You can use it to migrate your entire Home folder. MA cannot be used for making selective copies. It is not a backup/restore utility.
If you create a new user account with the same user/short name, then you can simply copy your documents and other files/folders using drag and drop. Since both drives have the same account owners and permissions there are no problems arising from copying data.
You could also accomplish your goal using a backup utility that would allow you to select what you want transferred. A good choice is Carbon Copy Cloner - VersionTracker or MacUpdate.

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