In 'my' case I have them all as SSD {Apps + OS/128GB} and RAID 1 HDD {Data/1TB}, and set to RAID. RAID treats the drives as 'AHCI' + TRIM for the SSD.
When building, I have an indifferent attitude and if I run into an install issue I don't think twice about reformatting, Flashing either the MOBO or SSD/HHD if needed. I never connect more than the minimum drives and I install all the header stuff last {USB/drive lettering}. After the OS is running then I'll configure RAID, CF/SLI, etc. If the Build is very complex then I bench build and once running -> install in case.
IF you want to use SATA2 then I would recommend using the first (4) four SATA2 Ports SATA1~SATA4; I always recommend the {Primary(ies)} be located on the first SATA Ports.
As I said if you're stuck on using a HDD on SATA3:
Failure: Install 'fresh' see item #4 use the SATA2_1; get up and running then install the LATEST Marvell driver - from Marvell {see right column} ->
http://www.marvell.com/support.html
Move to SATA3 Marvell Port.
The speed differences of IDE vs AHCI and HDD {not SSD} are negligible, so unless I needed a hot-swap HDD and an SSD I would probably run IDE in your case. But you 'seem' hell bent on eeking every ounce of performance so AHCI was my recommendation.
RE: "H50/H70 pump" the step I apparently omitted was Load Defaults; too many posts. If you had a Corsair H50/H70 then you want the pump running 100% always.
http://www.newegg.com/Product/Product.aspx?Item=N82E16835181013 a lot of X58 people run the Corsair; I said "if using..." operative word IF.
*. BIOS: Load Defaults
1. Set-up the BIOS: IDE->AHCI {OPTIONAL} [strike]; if using an H50/70 'pump' to the CPU_FAN header-> CPU FAN 100%. [/strike]
2. (1) O-N-E HDD and DVD
3. Never have a DVD installed in SATA2 first 4 ports or with AHCI
4. FULL Format HDD; use a utility if you need to wipe the HDD
5. Boot order 1 = DVD, 2 = HDD
However, my real opinion of what 'I would do' was clear from my first post.