Mountain Lion re-install has migration assistant options greyed out.  How do I choose only data I want?

I ran out of space on my Mac Mini so I bought the iFixit kit and added a second drive.  This resulted in me putting a 60GB SSD system drive and a faster 7200 RPM 500GB data drive in the mini.  I removed the original 500GB drive and placed it in an external enclosure.
After installing Mountain Lion I ran migration assistant.  It shows all the data from the external drive, but everything is checked and it will only migrate to my 60GB OS drive.  Of course this won't work.
I made a link to /Users to my second internal data drive but migration assistant still shows a -486.34GB of space needed.
So, instead of taking a week to upgrade my App Store purchases and install and configure everything (Mountian Lione Server, Xcode, Microsoft Office, Parallels...) how can I get migration assistant to allow me to just choose specific items to migrate?
As a side note, how can I make Mac OS X Mountain Lion use the second internal drive for User accounts *AND* recognize it properly?  My link works but I'm early into this and would rather do it 'right' now then live with frankenmac later.
Thank you,
-Tim

Well, maybe I posted to the wrong forum... 
I went in to speak with a mac genius too.  All I got was, "In all the years I've worked on Macs, I've never seen the migration assistant with greyed out options."  Ok.  I guess I have more experience, I've seen it.  They then suggested I run check permissions on the drive and buy Disk Warrior for $100.  Sorry guys, the drive is fine.  My TM backups are fine.  It's not that.
I went ahead and bought a 1 TB drive.  Even then, the migration assistant choices were greyed out.  I went ahead and created a Fusion drive to take advantage of the SSD (the 1TB is only 5400 RPM).  The directions can be found here.  I then just ignored the greyed out options and brought *all* the data over to the 1.1TB drive.  Everything works fine.
I'm bummed about not getting the apps and O/S pinned to the SSD but I figure if anything is getting used a lot, its where it needs to be.

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