Hello and welcome to the forum !
First of all, make sure that you update the firmware of your 7K3000 2TB to the latest version (800) with this DOS updater tool (if it doesn't work, try switching AHCI to IDE mode=compatibility mode for the updater to work):
https://apps.hitachibackup.com/d/?PGUSXJVM
Then, here are the answers:
1. You need the latest (but not official) Hitachi Tool v. 2.16 M2, which I uploaded here:
http://www.freefilehosting.net/ftool216m2sata60support
It does have SATA 1.5/3.0/6.0 gbps support, so you can set any of these. You will also have a Spread Spectrum setting. Do not set that (the factory default, Disabled, will remain) or if you still want to set it, set to Disabled.
In your case, the best idea is to set the drive to 3.0 gpbs and leave Spread Spectrum unset. It looks like your motherboard can't properly negotiate to SATA 3.0 gpbs and drops it to the slowest connection, i.e. 1.5 gpbs.
2. I think you will not have any problem with dropouts with firmware 800. If you do, you can try reverting the firmware to 5C0 or even to 580 (I have them in case you need them).
I have no idea how to specifically set CCTL on 7K3000.
However, I've had some issues at one point with CCTL (equivalent) on Seagate 7200.11 and noticed that Spread Spectrum was directly related to dropouts. So you might want to inform yourself on the Spread Spectrum feature on these Hitachi drives and how it relates to CCTL and/or dropouts and UDMA CRC errors. In my case the UDMA CRC errors in SMART are gone since updated to FW 800.
I have never tried to Enable Spread Spectrum, so be very careful with ever doing so, you might not get your drive recognized anymore...
3. In the Feature Tool 2.16 you will also find an APM feature (Advanced Power Management).
If you set it to 254 or Off, then the heads will always stay on the platters, there will be no head parkings. The drive will have the highest power consumption, will heat more (5-10 degrees extra) and if shocked, the heads might scratch the disk.
If you set APM 128, then the heads will park after about 25 seconds, the platters will continue to spin normally. This will consume less power and the heads are relatively safe.
For APM < 128, the heads park and the platters spin down after 25 seconds of inactivity. I won't recommend this though.
For the 7K3000 model, you will hear a high-pitched screeching noise when the head comes out of parking and is loaded onto the disk. It is normal, don't worry. I've seen that on all 7K3000 drives if APM is <=128.
Hope this helps,
Keep us informed how it went.