I think we need to clarify what a true "clean install" is. If you wipe the entire drive and reinstall the OS, none of your data is going to be there. No mail, no iTunes music, no bookmarks... nothing. All you will get back is what you manually move back piece by piece from a backup source or pull in over the network (Internet/iCloud).
If you use the Time Machine restore option that WILL bring back all your settings and data, but also completely defeats the purpose of the clean install, and is not really a clean install any longer. If there is a system setting or application setting that is causing you problems, doing a Time Machine restore just puts that problem right back on your machine.
Apologies if you already understood this, but from your questions it appeared there may be a little confusion?