Installing New Hard Drive for New OS

I have a MBP (late 2008), and have loved it since I first acquired it.  I am currently running OSX Lion 10.7.4, and I plan on upgrade to Mountain Lion when it is released.
My MBP came with a 250-gig HD in it.  I am wanting to swap it out for a 500 Seagate Hybrid drive before I install Mountain Lion.  My current hard drive is backed up on a 1-T external drive using the Time Machine app. 
My question is this...I have never restarted a Mac from scratch. Prior to my current MBP, I used PC.  (Praise the Lord for discovering Mac!)  As a PC user, it took the largest part of a day to backup, reformat, and reinstall programs and drivers.  Are there any tips that you may offer on making the installation of a new drive a simpler task.
Questions:
1.  Will it be better to install Lion and then upgrade to Mountain Lion, or should I just install the new version straight?
2.  Will Time Machine be able to reinstall everything on my drive as it was, or do I have to reinstall each app?
3.  If I have to reinstall apps, what is the best way to handling the licensing registrations for various apps like Adobe CS5.5, iWork, Office 2011, etc.
Thank you for any advice for making the transition to a new drive an easier project.
Pastor Wynn

Well, he's taking the easy way out - I know from my various cloning tests and from talking to others is that at first (after Lion was introduced), neither SuperDuper nor CCC could clone a recovery partition - the reasons: the recovery partition is a separate partition and only one partition can be cloned at a time and second, this partition is hidden and as such can't be cloned. Since then, CCC has added the capability of restoring/adding it.
SuperDuper can't do it, so they want you to waste several hours and bandwidth downloading and installing the entire OS again. You can download it without having the recovery partition (since you can download it as often as you want), but it's not quite the same process. Yes, it will restore the recovery partition, but, if you won't use it because you don't want to spend hours downloading it, then you don't really need it except for repair purposes or in an emergency.
I've tried different ways of restoring and backing up and personally, I don't like to have to download/install it again (although I've done it). I prefer being able to rely on my clone - no internet connection needed. But, since the recovery partition also includes the old Disk Utility capabilities of repairing your hard drive (without having to boot off another drive), I do want that as well. So, for now, it is CCC for me including creating a recovery partition.
I think I'm the last person on the planet who has never used the Apple App Store.
Aside from downloading OS/Lion/updates, I have never used it, so you're in line right with me.
And, I've never done a block level clone because your destination drive needs to be the same size as your source which, in my case, is ridiculous: my internal is 1 TB but I'm only using 100 GB of that right now. So I'm supposed to "waste" 800 - 900 GB empty space of an external drive to get a block level - I decided a regular clone is fine and I have my externals split into 5 - 6 partitions each containing 2 clones of each OS and machine I have.

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