My 2009 Macbook Pro Core 2 Duo is running 10.7.4. It feels sluggish and their other problems which are unsettling. I have a MacPro 8core Nehalem that I'm using for Avid Media Composer. I did a "ground up" reinstall of selected apps onto a new 10.7.4 OS. It has increased the performance and reliability. I want to do a similar re-install on my Macbook Pro. Very time consuming and several questions have arisen. This thread has nothing to do with migrating files or apps between the Macbook Pro and the MacPro.
One of the problems with my EXISTING OS is
I started out by installing Lion onto an external FW 800 BUILD device. Its a Lacie portable bus-powered pocket drive. I did all upgrades to the OS. Then I migrated from an OS that only contains Final Cut Pro, and no other documents or apps. FCP launched fine with my S/N and then from that point I manually installed about 20 apps one by one.
I see John has you covered.
I suggest you follow his advice and not create Applications within the user account. Once you clone the new build back to the computer drive, test to make sure it's working properly. If you want to migrate the user back from the old build, it will have to be a different user name than the one you created on the new build. If it is, then just migrate the user and settings and do not choose to migrate applications.
You will gain no advantage by having seperate copies of Applications. Each user will have access to the Application folder and each can create and have it's own settings for the applications.