How do I transfer everything from iPhone 3GS to my new iPhone 4S?

Question

I purchased an iPhone 4S to replace my iPhone 3GS (which I will keep for spare, other chores).  What I assumed I could do (and it seems I accomplished when I had upgraded from a 3G to 3GS) was that there was a way to restore my 3GS backup to the iPhone 4S.
So, as a first step, I upgraded the 3GS to iOS5, made sure everything works OK, then did a backup of the 3GS through iTunes to my computer.
When I connected my new 4S to my computer/iTunes and registered it to iTunes, I looked for a way to restore my 3GS apps/setup to the 4S.  I could not find a way, but as I was looking I noticed that iTunes was automatically attempting to install every single app I had ever downloaded or purchased, some 400 of them.  By the time I was able to stop it (by canceling, then changing settings in iTunes so it would not try it again), 100 apps had been loaded, most of which I no longer use.
I have not had time until today to get back to this project, and meanwhile have been using my new 4S, sync'd to my MobileMe account for my Contacts, Calendars, and mobileme email account.
Just now I started searching on the Apple website, came to a box to type in my question, and it had me sign in and start this email query - so hear I am...
One more thing, I tried setting up the 3GS on iCloud (using my iTunes account ID, which is different from my mobile me ID), and after it appeared all docs and data backed up, set up my new 4S on the same iCloud account, but switching on backup did nothing.

Answer 1

Almost there...
I'm replying to myself, as I have found the answer.
1.  Started iTunes, connected iPhone 4S, turned on Airplane mode.
2.  In iTunes, hovered mouse over my iPhone 4S name in left column, in popup box clicked on "Restore from Backup..."
3.  From menu clicked on name of my old iPhone 3GS backup.
4.  Backup appeared to be finished in about 8 minutes, but I new that could not be correct...iPhone had rebooted, so I entered password.  I could see that most apps were "waiting" and grayed out, also in iTunes top status box indicated that apps were being sync'd.  Also noted that my iPhone 4S now had the same name as my "old" iPhone 3GS. 
5.  After some time (a couple of hours, perhaps, not sure because I went to sleep), everything appeared sync'd on new iPhone, and iTunes stated that sync was OK.
6.  Manually renamed my new iPhone 4S to its correct name, then backed up to computer.
I decided to hold off on iCloud for now - two majore issues:  1) have heard some reports of data dissappearing, and 2) I will have to talk to Apple about MobileMe instructions for moving to iCloud, which state that move will not transfer my mobileme email, and also that I cannot install iCloud management software (nor sync to Outlook) on my Windows XP computer - I intend to upgrade to a new Win7 in January 2010, and I have heard it is not so simple to change iTunes/device syncing to another computer.  Sounds like a good project for the Christmas-NewYear holidays...