Clean install and selective migration?

Hi,
First a bit of background:
I have 2 Macs, a 2009 Mac Pro and a Late 2011 MBP 17".
The Mac Pro was originally Leopard, then Snow. I decided it was getting risky and upgraded to 10.8.5. No issues.
The MacBook Pro came with Lion. I wanted to upgrate that to 10.8.5 too. Oh my goodness what a nightmare!
In brief: Upgraded MBP to ML. At the same time it did a firmware update for Thunderbolt. Ever since this, it proves very hit or miss with booting – it tends to hang before the login screen (spinning beachball of death). I have done all the SMC and NVRAM resets, and eventually did a clean install of Mountain Lion, then used Migration assistant to copy everything from the MacPro. It still seems to have issues. Apple tech support say that it cannot be software if I've reinstalled everything, but they did say I should NOT have migrated the users over. Not sure why.
Anyway, I took it in to an authorised service centre and they said it could be the HD on its way out (although SMART status is ok). They recommended that I replace the HD with an SSD. However, as I have loads of client and personal data on my HD, I cannot send my MBP away for someone to clone etc, and dispose of the old HD without me knowing how well they disposed of it.
So, I've just secure formatted the whole machine. When I came to restart, it wanted to install Lion rather than ML. I was surprised, as I'd heard that once you update the OS, the firmware gets rewritten so you can't go back. Anyway, I loaded Lion, then reinstalled ML. So now I have a clean install on the HD. I did this so that when they swap the HD for the 1TB Crucial M500, they can set me up with ML all ready to go, not give me back a Lion machine.
So, anyway, with all that as preamble, these are my questions:
1 - The Apple tech said that I should not migrate users. But I do want to get all my email history etc back. If I migrate "data", will I be able to create a new user and get it back to how it was?
2 - Applications-wise I personally would rather rebuild from scratch as my Mac Pro has got so many out of date apps that I don't really want to migrate, but what I'm concerned about is that I cannot find my MS Office 2008 disks, so ideally I'd like to migrate that. In other words, is it possible to choose which apps I migrate across using Migration Assistant?
Or am I really going to be forced to migrate users, apps and everything? And does anyone know why Apple tech think this might be the cause of the problem?
Sorry, I lknow that's a lot to read but I always think background info is useful.
Thanks in advance. I'm off to take the MBP in to have the SSD fitted, but will need your advice for setting it up when I get it back.

A few things...
1. Updating the firmware doesn't preclude loading an older version of the OS. Depending on the machine and the firmware, it may set up Internet Recovery with something different than what you're installing. For example, the firmware update may set up Lion as the Internet Recovery system, then you install Snow Leopard. You can do it, it's just that if you use Internet Recovery it'll use Lion.
2. Your problem could be the hard drive, or it could be the SATA cable. The way I normally test this is to move the drive to an external enclosure and boot from it by holding down the Option key and selecting it. If it runs fine from there, the SATA cable is the problem.
3. You really don't need tech support to do this, it's all pretty straightforward. By all means use them if you're uncomfortable doing this kind of thing, but the problem is you may get it back with the same problems. Especially if it is a SATA cable, as an SSD is only going to give you more errors than the HD did.
4. Migration Assistant gives you the option of moving Applications, Data, or Settings. You can move any or all of those categories, but not selectively. If you move Applications it'll move all of them.
5. As far as not migrating users... the reason to not do this is in case there's some software loading for the user that's causing problems. An easy way to find out if that's the case is to set your machine up with a clean install then clone it with something like Carbon Copy Cloner to an external drive. Now do your migration. If the migration causes problems, just copy the clone back onto the drive.
Here's the procedure for changing a drive in your model:
http://www.ifixit.com/Guide/MacBook+Pro+17-Inch+Unibody+Hard+Drive+Replacement/3 401

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Message was edited by: donv (The Ghost)

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TJ Skywasher wrote:
Someone suggested clean installing OS X and then using Migration Assistant to load all my data back on from a Time Machine backup, but customise what I want to restore.
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Hello apple community,
This is my first post ever, so here goes nothing..
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Clean install and selective migration?

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