Migration Assistant issues and losing files (Mt. Lion on new hard drive)

I just, by either dumb error or providence, migrated the contents of my backed up hard drive, which has my Mt Lion and all applications folders, to a new hard drive. The old and original drive on my 2008 Quad Mac Pro was starting to worry me. All of the applications and systems files appeared to have migrated flawlessly, and my calendar updated and my 20,000+ emails were restored. All of the programs/applications work. Everything appears normal, except data and obvious missing files. (Note I had installed Mt. Lion over  Leopard and Snow  Leopard previously, and did not rewrite the drive before I did that.)
The size of this new drive is substantially less than the last one. On the latter, I counted more than 50 gigs of data, on the volume with all of the primary OSX documents. That is what I see in the Time Machine backup right before I did the Migration Assistant. The size of the same volume on the restored new hard drive that has my OSX is about 31 gigs.
I did NOT run (by accident and perhaps curiosity) the Time Machine restore backup using disk utilities. Again I did, by accident or curiosity) Migration Assistant.
What does appear lost are all of the Windows documents that were accessible on my portioned drive on my old hard drive, accessible only via VMWare. (I had all of those previously backed up, brute force, before doing this, and I'm not worried if I don't access them now since I have them if I need them). This was about 18 gigs of data I guess.
Does anyone else have experience with using Migration Assistant and losing files that may have been on a partitioned drive (running Windows) and accessible by VMWare? I can still rewrite over the new drive I just formatted and do it all over again using disk utilities and running this from a boot jump drive I created before, but this time using Restore/Time Machine. I just had heard from one source it was best to download Mountain Lion first, and then do a Time Machine restore, which I ended up actually not doing.
Thoughts appreciated.

I just, by either dumb error or providence, migrated the contents of my backed up hard drive, which has my Mt Lion and all applications folders, to a new hard drive. The old and original drive on my 2008 Quad Mac Pro was starting to worry me. All of the applications and systems files appeared to have migrated flawlessly, and my calendar updated and my 20,000+ emails were restored. All of the programs/applications work. Everything appears normal, except data and obvious missing files. (Note I had installed Mt. Lion over  Leopard and Snow  Leopard previously, and did not rewrite the drive before I did that.)
The size of this new drive is substantially less than the last one. On the latter, I counted more than 50 gigs of data, on the volume with all of the primary OSX documents. That is what I see in the Time Machine backup right before I did the Migration Assistant. The size of the same volume on the restored new hard drive that has my OSX is about 31 gigs.
I did NOT run (by accident and perhaps curiosity) the Time Machine restore backup using disk utilities. Again I did, by accident or curiosity) Migration Assistant.
What does appear lost are all of the Windows documents that were accessible on my portioned drive on my old hard drive, accessible only via VMWare. (I had all of those previously backed up, brute force, before doing this, and I'm not worried if I don't access them now since I have them if I need them). This was about 18 gigs of data I guess.
Does anyone else have experience with using Migration Assistant and losing files that may have been on a partitioned drive (running Windows) and accessible by VMWare? I can still rewrite over the new drive I just formatted and do it all over again using disk utilities and running this from a boot jump drive I created before, but this time using Restore/Time Machine. I just had heard from one source it was best to download Mountain Lion first, and then do a Time Machine restore, which I ended up actually not doing.
Thoughts appreciated.

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