Also, can you clarify what you mean by 'it is not bootable'?
It means that you cannot use it to boot up your computer.
With a bootable clone, you can - you start up and hold the Option key and the Startup Manager will show you which disks are available for booting - your clone should show, so you choose that and boot up.
By install the OS first and then port over my files, do you mean by using the 'migration assistant' as opposed to the 'install with a disk' option? There is nothing I would like to 'exclude' or change so would just starting the process with the disk to begin with, as opposed to using the 'migration assistant', be the better option?
Not sure what you mean with the "disk"? I am referring to your external drive which has your backup. You can actually also use your old Mac and connect them using target disk mode (that is what I've always used):
http://support.apple.com/kb/PH13842
Personally, I've found that the easiest way.
When you first turn on your new Mac, you can use the Setup Assistant which is by far the easiest way to port over files - you need to follow the onscreen instructions and connect the two machines. If you wait until later, it will be Migration Assistant and it will create a second user account for the transfers because you've already created one. You will then need to deal with getting rid of duplicates.
I don't have to 'de-activate' anything on my old laptop, right?
Yes, you do. You need to de-authorize it in iTunes and you need to wipe it and reinstall the original system before selling it as anything you've obtained at the app store is tied to your Apple ID and not transferable.
http://support.apple.com/kb/HT5189