How do I fix Hard Drive Bottle Necking?

I'm running:
SanDisk 480gb SSD - OS
6 3TB Western Digital Internal 7600RPM Drives
Intel i7 4770K Haswell 3.5GHz CPU
MSI Z87 XPower Mobo
3 MSI Gaming N760 Video Cards (Running in triple SLI)
32gb G. Skill Trident X RAM
Windows 7 Ultimate 64-bit
Right now I'm rendering a 3:04 project and it's barely halfway after two hours. Seems like the remaining time stays at 1hr 30mins indefinitely. I don't think it's a processor issue as it's only running at 15% right now and my RAM is running at 60% right now (this is with other apps running). So I think my problem is the hard drives. I need to learn or find out how I can utilize my disks more effectively. Can I install another SSD strictly for Caching? (Also, how would I setup AE/PP to do that?).
The project, media, and render output are going to the same drive which I'm pretty sure is not optimal. But, I don't know any better and can't find the information I need on the forum or on the web. Can someone post links or tell me what the best way to setup my projects would be? Obviously I have plenty of space to arrange this however would be best. Any help is awesome!

After Effects CC 12.0.0.404
Windows 7 Ultimate 64-bit Service Pack 1
No Thirdparty Hardware
Issue occurs with single video layer 3m 04sec, Used Keylight 1.2 to Take out the green screen, Footage is H.264 in a .mov container with an alpha layer
No error messages (Just Slow)
This issue occured while rendering footage from AE in AMC
It worked fine before, nothing changed on my system
I have quicktime installed Version 7.7.4
No other software was running before issue started only AMC
No third party effects or codecs installed
I have no idea what OpenGL even is.
This only occurs when rendering.
I am using multiprocessing, I have 6 cores dedicated to adobe products and 2 cores for background applications
In AE: File > Export > Add to Adobe Media Encoder Queue

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How do I fix Hard drive errors on my macbook pro?

I ran the etrecheck software on my Macbook Pro and it produced the following results. It says there are 15 errors with the hard drive and I was wondering how I can figure out what they are and possibly find a solution to get rid of them. I have used the disk utility to verify and repair permissions and to verify the disk and the only issue i get during that is this warning during verifying permissions:
Warning: SUID file “System/Library/CoreServices/RemoteManagement/ARDAgent.app/Contents/MacOS/ARDAg ent” has been modified and will not be repaired.
I also should mention my computer has been running slower than normal lately.
Another point is that there is a user launch agent that fails and I was wondering if I need it and how I can fix or get rid of it.
If anyone could help me out or point me in the right direction, I would greatly appreciate it.
Thank you,
Joe
EtreCheck version: 2.1.8 (121)
Report generated March 23, 2015 at 12:28:35 AM EDT
Download EtreCheck from http://etresoft.com/etrecheck
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Hardware Information: ℹ️
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    MacBook Pro - model: MacBookPro6,2
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    8 GB RAM Upgradeable
        BANK 0/DIMM0
            4 GB DDR3 1067 MHz ok
        BANK 1/DIMM0
            4 GB DDR3 1067 MHz ok
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    NVIDIA GeForce GT 330M - VRAM: 256 MB
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        EFI (disk0s1) <not mounted> : 210 MB
        Recovery HD (disk0s3) <not mounted> [Recovery]: 650 MB
       Macintosh HD (disk1) / : 318.84 GB (105.13 GB free) - 15 errors
            Core Storage: disk0s2 319.21 GB Online
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        My Passport for Mac (disk2s2) /Volumes/My Passport for Mac : 999.83 GB (238.82 GB free)
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Backup your computer. You may have to replace the HD.
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Hard Drive bottle neck.   Running SRT thinking of switch to SSD

I did the "windows experience index" on windows 7 on my new custom build. I got 7.9 (which is the best score) on everything but the primary hard disk. I got a 5.9 score for the primary hard disk.
I set up the drives with Intel's SRT with one 120 Patriot Wildfire Sata 3 drive (only using 60 gigs of it I am using for the SRT seeing that is the max and the other 60 gigs I partitioned it for extra storage space) and a 1 teribyte HDD sata 3 in the two sata 3 ports on my Gigabyte motherboard.   My Media drives are two 1.5 tb in a Raid 0 in the two Sata 2 slots but i don't think the "windows experience index" uses those in their test.
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www.brentdolanmedia.com

Thanks everyone for your input.   I think for now I will just leave the system the way it is. Why mess up a good thing right?
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I edit in AVCHD footage.   The footage edits great. Alll real time play back. Exporting to a H.264 is basicly in real time (10 minute clips exports in a little under 10 minutes)
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How do i Check Hard Drive space in OS X Mavericks?

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******Clicking the Thumbs-Up button is a way to say -Thanks!.******
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How do I fix Hard Drive Bottle Necking?

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