You cannot migrate a JBOD unit disk into a raid 1 mirror.

You must deselect export JBOD policy in the 3ware controller first. Once you do this the disk in question will remain as a "JBOD" unit and not automatically be considered a "single disk." According to the RAID level migration chart that is linked to in the question, the Single Disk Unit is migrate-able to a mirror "unit." In order to migrate the disk, you will need to delete the unit and recreate it. The disk will be updated to "Single Disk." To complete this change the partition table on the disk will be wiped.

Essentially there is no direct way.

However you can use partimage to make a disk image back up of the your windows boot drive (in my case my desktop Windows 7 x64 Professional disk configuration has a partition configuration as follows: sda1 [110mb as boot] and sda2 [110->1000GB as c:\ system drive]). Use this backup to restore to your raid 1 mirror disk after it is created.

Note: Make sure that you use a partition backup/restore utility that allows you flexibility in restoring images of partitions to larger or smaller target partitions. Otherwise you can run into this problem that I ran into using partimage:

http://www.partimage.org/forums/viewtopic.php?p=2784#2783

If you run into this problem with partimage, or with another disk image utility, you're going to have to follow the steps I've outlined here to resize the partition backup before being able to restore it:

https://serverfault.com/a/365145/111963

Do yourself the favor of resizing your partitions to the smallest possible size using parted before you create your partition backups so that you don't end up having to jump through hoops to restore your data. Keep in mind that Partimage is old and development on it has stopped, unfortunately I did not know this. The Linux Rescue CD (which btw works very will with the 3ware 9650) includes this old software that you can use successfully to take partition backups. Partimage like CloneZilla has network backup features if like myself you only have two disks available to play with.

The best way to migrate your disk then is as follows:

1. Boot to a rescue cd that has parted or gparted and either partimage or clonezilla.
2. Resize BOTH your BOOT partition (SDA1) and your windows partition (SDA2) to the smallest possible size using gparted. This will not only resize the partition but the filesystem itself will be shrunk as well, remember this for step 8.
3. Take the backups of these partitions, I used partimage, because I needed to send the partition back up image files to a network server, CloneZilla has this capability and still enjoys active development. Make sure you read the limitations section of the CloneZilla page.
4. Once you are confident that you have backups of the mbr and all partitions on the disk:
5. Use 3ware bios raid manager to delete both units (jbod and single disk) and merge into single raid 1 unit.
6. Boot to rescue CD again and use parted to recreate the partition table and the partitions to the original full size configuration. (you'll noticed that your 1 Terabyte drive and useable disk space is somewhat smaller than the original single disk).
7. Because you now have full size partitions, the backups you took of the resized smaller original partitions should all restore with no problem.
8. Because the file systems that have been restored to your full size partitions reflect the maximum partition size of the shrunk partitions (steps b and c) you may need to resize the filesystem to take advantage of the rest of the space on each partition. Clonezilla should resize the filesystem for you when restoring the image. If it doesn't then you will need to resize it yourself. You can use Windows Vista/7's built in resize option. In Linux you can use ntfsresize.

I managed to get the RAID to rebuild by issuing the following command in tw_cli without pulling any drives or rebooting the system:

/c2/u1 set ignoreECC=on

The rebuild didn't proceed immediately, but at 2 AM the morning after I made this change, the rebuild started and about 6 hours later, it was complete. The drive with ECC errors had 24 bad sectors that have now been overwritten and reallocated by the drive (according to the SMART data). The filesystem seems intact, but I won't be surprised if I hit errors when I get to whatever data was on those sectors.

In any case, I'm much better off that I was before, and will likely be able to recover the majority of the data. Once I've gotten what I can I'll pop out the drive that's failing and have it rebuild onto a hot spare.