Protools 10 Severe issues - I'm newby here so please be kind :)

Hi, I'm currently working on several projects with various requirements of Protools intensity. The entire System is new and there are so many issues with it, I thought to post here and maybe someone can help solve one of them, or perhaps suggest what the core problem may be. This is the list of all the strange symptoms occurring. I know it's quite a lot but thought it necessary as they must be related one way or another.

We have separate System, Audio and Sample Drives running.
Mac Pro 12 Core 2.4, 12G Ram
OS 10.8.3
Protools 10.5.3 Native
Kontact 5.10.6
Apogee Symphony IO

Thanks in advance for any guidance.

1. - apple usb keyboard stops controlling tools* - Only save command works.
2. - apogee switching randomly (often sample rates)
3. - CPU error messages
4. - 'drive can't get audio fast enough - raise buffer size' error message*
5. - autotune/pitch correction latency at low buffer sizes (128)
6. - latency recording in large projects
7. - latency recording in small projects (<20 tracks) (on and off - no changes made in session an it alters between latent and not)* Disappears on reboot.
- latency with only one instance of Komplete 9* - Have tried every combination of Processor numbers in Tools.

This is 12 Core Mac Pro and is clearly not working to anything like it's potential. My MacbookPro is running rings around it.
Thanks all for listening. David