Migration Assistant not displaying relevant drive

I purchased a 1TB SATA internal HD for my Mac Pro tower last night, with the intention of making it my start up disc. Currently I have a 500GB HD in bay 1 of 4, with a secondary internal drive in bay 2. I put the new 1 TB into bay 3, slid the carrier shut, and launched Disc Utility and formatted the disc, no problem. I then launched Migration Assistant, with the intention of copying over all of my files from my 500GB current start up disc, over to the new 1 TB drive in bay 3. Afterwards, I was going to put the 1 TB drive into bay 1. Upon launching Migration Assistant, here is the first prompt that came up with two radio button choices:
HOW DO YOU WANT TO TRANSFER YOUR INFORMATION?       
• From another Mac, PC, Time Machine backup, or other disk?
Transfer information to this Mac from another Mac or PC on the same network, a backup disc, or another startup disc.
• To another Mac
Transfer information to another Mac on the same network
I selected the first radio button (top bulleted item above). I was then prompted to provide my password by M.A. When I did so, another window popped up with two more radio button choices:
HOW DO YOU WANT TO TRANSFER YOUR INFORMATION?       
• From another Mac or PC
Transfer information to this Mac from another Mac connected to it, or from another Mac or PC on the same network.
• From a Time Machine backup or other disk
Transfer information to this Mac from a back disk or another startup disk
Wanting to copy data over from my current startup disc, I selected the second radio button.
When I did so, the only choice I had was HD 2, which I didn't want, or a Time Machine backup of my startup disc (HD1) which was done too long ago to make it a currently relevant.
The big question is, after an hour of waiting for all the drives to be scanned, why wasn't the startup disc (HD1) offered on the list to choose from, instead of just the Time machine backup version of that same disc?
Would placing the new 1 TB drive into bay 1 instead of bay 3 solve the problem?
Thanks, Carl
p.s. Using Lion 10.7.1

Thanks again, John.
While I was waiting for another reply, I tried something I had heard about that seems to have worked. I rebooted into Lion's Recovery Disc. I then launched Disc Utility and selected the Restore tab. The resulting window gives you a source disc field and a receiving disc field. I just selected the existing 500 GB startup as my source and my new 1TB drive as the receiver and hit restore. It copied file for file the entire contents over to my new drive in about an hour and a half. I renamed it HD 1, dropped it into bay 1, renamed HD 1 as HD 2 moved that into bay 2, and so on with the last internal drive. I set the startup disc in my Pref Panes as the new "HD 1".  It started up and remembered my username and password. So far, so good. Why do I get the feeling there's another shoe to drop? Maybe it's just my paranoia.
Carl

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