Clean reinstall of iTunes and APPROPRIATE apps for iPhone 3GS?

Hi Guys,
I know it's been asked before (sorry) but I would value everyone's opinion and answering a couple of questions
to avoid messing up.
I want to clean erase my iPhone 3GS and also ensure I get the correct iTunes default folder structure setup in Windows by doing a
clean iTunes install.
What I would like to do is fourfold:
A. Backup contents of iTunes
B. Total erase and restore iPhone to default.
C. Copy back most (but not all) of my media
D. Copy back only apps that will work well on 3GS. (avoiding apps that may have inconsistencies with 3GS or OS4)
Questions:
A. Before I reinstall the latest iTunes, I presume all I need to do is move the whole of the
   iTunes folder structure to another safe place like the desktop, where it can be used as a backup?
B. I figure it's easy to carry out a total erase of iPhone is easy but do I need to do anything like unauthorise phone or iTunes before I do all this?
C.I then intend to create a subfolder e.g. New wave, and then drag each relevent music file to the relevent subfolder - Or is that not a good idea?
   i.e. Is it best to just let Playlists sort the categoeries?
Finally, do I simply select Add Folder in iTunes and add all the music folder to the library - or will that create duplicates?
D. I have a large number of apps purchased through the Apps store.
    I intend to drag and drop these in the Mobile Applications folder. Is that a good idea?
    Is there a quick way to ensure each app is compatible with the latest OS, the latest iTunes, and my iPhone 3GS?
Thanks guys in advance
Pete

Sounds like a lot of work and complication for little or no benefit.
Concerning the Apps.... there is no need to manually go through the list and add specific apps, just tell iTunes what you want to sync to the device and what not to sync. All of this is handled IN iTunes, no reason to try and deal with it elsewhere.
As for the music, if there is content you no longer want, delete it.
Is the music folder currently unorganized?
I just see no reason, based on your posting, to undertake this enormous task.

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