getting rid of a RAID controler

Hello,

I have a server, far away in a datacenter, running FreeBSD 8.1. The server has a PCIe 3ware 9650SE-4LPML RAID controller.
The configuration is this one: 

RAID 1, 2 disks : System, binaries, and some user data
JBOD/Passthrough, 1 disk, user data
JBOD/Passthrough, 1 disk, user data

/, /tmp, and /var are UFS
/usr/local, /usr/ports, /home are ZFS

I want to get rid of the 3ware and plug my HDDs on the motherboard, so I'm facing few challenges:

- how can I make sure HDDs will be recognized natively when they are not "served" by the RAID controller?
- how can I make sure I can boot from one of my mirrored HDD?
- how can I recreate a RAID 1 array from the 2 mirrored HDD?

I know I'll have to edit /etc/fstab, and export/import ZFS.
I know the 3ware controller reserves the first Mb on each HDD to write info/config about arrays.

I can spend only limited time in the datacenter, and have to plan a long time ahead for each visit, so the most I can do remotely, the better it is.
I'm thinking about this scenario: 

0- export ZFS pools
1- break mirror: plug HDD "A" to motherboard, leave HDD "B" on RAID controller, boot from "B"
2- format and partition "A" to prepare for a software RAID (gpart?), rsync data from "B" to "A", tweak fstab on "A"
3- remove RAID controller, plug HDDs "B", "C", "D" to motherboard, boot from "A"
4- format "B", add "B" to software RAID, reconstruct mirror
5- reboot from A+B RAID 1, import ZFS pools

Any piece of advice is welcome, anybody who has some experience in that field is welcome. I've used gpart only once, copy-pasting from a tutorial, and I don't know how to deal with the creation of a "one hdd RAID 1 array" (step 2).
I don't know if my HDDs will be recognized without formatting ("C" and "D").
If it's absolutely sure they are recognized without a format step, I guess I can just export ZFS, change fstab, plug all HDDs on motherboard, reboot from one half of the mirror and do everything else remotely.

thanks,
Patrick