Reinstalling Mac OS (Lion)

So I ran into a problem with my boot camp partition (it became corrupt for whatever reason).  I used the boot camp tool to remove the partition in order to recreate it and reinstall Windows, but it failed (Windows was gone and I'm back to a single partition, but the space did not release).  I have verified this by doing the simple math (adding 10% or so to my final calculation) and the questionable missing space adds up to the size of the boot camp partition I had created.  Interestingly enough, the recovery partition is missing now too.
Research in the support community shows a rebuild is the way to go to fix this.  Being a long time Windows guy (actually employed running a data center with many Windows based servers) and this being my first Mac, I wanted to make sure I had a good handle on this.  I bought my MacBook with Snow Leopard installed and upgraded to Lion when it was released.  When Apple originally offered the tool to create a Lion Recovery disk on a USB drive, I did it (and now am very glad that I did).  Here are my questions:
- Should I erase and reformat the disk or is that done as part of reinstalling the OS?
- Do I need to install Snow Leopard and then upgrade to Lion or does the Lion Ugrade USB Recovery disk take care of this?
- I have a good backup from Time Capsule.  Does it only restore the files/photo's/etc. or does it restore app's as well (remember, I'm a Windows guy and the idea of an application not needing to be reinstalled is kind of a foreign concept to me).
I appreciate any assistnace.  This looks to be a simple process, but I didn't want to start, run into a problem, and have to visit the Apple Store (at a time when the phones are causing over-crowding at the stores).

Well, bootcamp and Lion Recovery HD have been know to create problems.
You can see if there are other hidden partitons by entering the following in Terminal:
defaults write com.apple.DiskUtility DUDebugMenuEnabled -bool YES
Then open Disk Utility and select Debug->View all partitons
You can try a complete clean re-install.
First, BACKUP to Time Machine or a Clone
Then, create a Recovery USB with: Lion Recovery Disk Assistant
Then boot with your Snow Leopard Install Disk, select from the Menu Bar: Utilities->Terminal and enable the Disk Utility Debug Menu with:
     defaults write com.apple.DiskUtility DUDebugMenuEnabled -bool YES
Exit Terminal and select from the Menu Bar: Utilities->Disk Utility
Select Debug->View all partitons (you should see the Recovery HD Partiton)
Select partiton, and create 1 Partiton (which will wipe your drive)
Your Recovery HD Partiton should now be gone (and Bootcamp if it was there)
Now, boot from the Recovery USB that you created with: Lion Recovery Disk Assistant
Select Install OS X Lion
When prompted to transfer data from another Mac or a Time Machine or other drive, select the backup that you made.
(you can use your Time Capsule backup, see: http://support.apple.com/kb/HT4413)
Tony

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