Stuck at grey screen after reboot

I seem to be stuck at the grey screen after a reboot of my server. Here are the symptoms and I'm wondering if anyone has experienced them before or has some idea of where to look:
1) Over the last couple of weeks, I've noticed the entire system freezing up for 10-20 seconds. The spinning pinwheel pops up and when my office is really quite, it sounds like either a fan is starting on the system or a hard drive is spinning up. Note that I've turned off all 'spin drives down when possible' in energy savings.
2) After the 10-20 seconds, a bunch of disk activity occurs and everything goes back to normal.
I've tried repairing permissions, checking for errors with the drive, etc. I've got two drives striped in Raid 0 (yes, the system is backed up--so I'm not worried about loosing data).
After a recent software update, I had to reboot it, and that's where it got stuck. Could be something there for some time, but my server usually runs for months at a time, unless an update requires a reboot.
Thanks for any help or suggestions!

Could you be more specific about what disks you used to boot with and exactly what programs you ran...
I cannot seem to get it to boot from the "Admin Tools" disk using the "D" key.
Also, when booting from the "Mac OS X Server" disk I can access Disk Utility, but do not see Raid Utility anywhwere.

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Model Identifier:          MacBookPro5,5
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Total Number of Cores:          2
L2 Cache:          3 MB
Memory:          4 GB
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Hardware Information:
          MacBook Pro (13-inch, Mid 2009)
          MacBook Pro - model: MacBookPro5,5
          1 2.26 GHz Intel Core 2 Duo CPU: 2 cores
          4 GB RAM
Video Information:
          NVIDIA GeForce 9400M - VRAM: 256 MB
System Software:
          OS X 10.8.5 (12F45) - Uptime: 0 days 22:12:2
Disk Information:
          WDC WD7500BPKT-22PK4T0 disk0 : (750.16 GB)
                    disk0s1 (disk0s1) <not mounted>: 209.7 MB
                    Macintosh HD (disk0s2) / [Startup]: 749.3 GB (174.02 GB free)
                    Recovery HD (disk0s3) <not mounted>: 650 MB
          OPTIARC DVD RW AD-5960S
USB Information:
          Apple Internal Memory Card Reader
          Apple Inc. Built-in iSight
          Apple Inc. BRCM2046 Hub
                    Apple Inc. Bluetooth USB Host Controller
          Fitbit Inc. Fitbit Base Station
          Apple Inc. Apple Internal Keyboard / Trackpad
          Apple Computer, Inc. IR Receiver
FireWire Information:
Thunderbolt Information:
Configuration files:
          /etc/hosts - Count: 20
Kernel Extensions:
          com.avatron.AVExVideo          (1.7 - SDK 10.8)
          com.Cycling74.driver.Soundflower          (1.5.2)
          com.hzsystems.terminus.driver          (4)
          com.avatron.AVExFramebuffer          (1.7 - SDK 10.8)
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          HP IO: Path: /Library/StartupItems/HP IO
          M-Audio FireWire Audio Helper: Path: /Library/StartupItems/M-Audio FireWire Audio Helper
          M-Audio Firmware Loader: Path: /Library/StartupItems/M-Audio Firmware Loader
          MAudioMobilePreUSB: Path: /Library/StartupItems/MAudioMobilePreUSB
          rEFItBlesser: Path: /Library/StartupItems/rEFItBlesser
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          [System] com.adobe.fpsaud.plist 3rd-Party support link
          [System] com.adobe.SwitchBoard.plist 3rd-Party support link
          [System] com.barebones.textwrangler.plist 3rd-Party support link
          [System] com.bombich.ccc.plist 3rd-Party support link
          [System] com.fernlightning.fseventer.plist 3rd-Party support link
          [System] com.fitbit.galileod.plist 3rd-Party support link
          [System] com.google.keystone.daemon.plist 3rd-Party support link
          [System] com.m-audio.firewire.helper.plist 3rd-Party support link
          [System] com.m-audio.usb.firmwareloader.plist 3rd-Party support link
          [System] com.megacloud.helper.plist 3rd-Party support link
          [System] com.micromat.TechToolProDaemon.plist 3rd-Party support link
          [System] com.microsoft.office.licensing.helper.plist 3rd-Party support link
          [System] com.oracle.java.Helper-Tool.plist 3rd-Party support link
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          [System] PACESupport.plist 3rd-Party support link
Launch Agents:
          [System] com.adobe.AAM.Updater-1.0.plist 3rd-Party support link
          [System] com.google.keystone.agent.plist 3rd-Party support link
          [System] com.gopro.stereomodestatus.plist 3rd-Party support link
          [System] com.hp.messagecenter.launcher.plist 3rd-Party support link
          [System] com.micromat.TechToolProAgent.plist 3rd-Party support link
          [System] com.oracle.java.Java-Updater.plist 3rd-Party support link
          [System] com.wacom.pentablet.plist 3rd-Party support link
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User Launch Agents:
          [not loaded] com.adobe.AAM.Updater-1.0.plist 3rd-Party support link
          [not loaded] com.adobe.ARM.[...].plist 3rd-Party support link
          [not loaded] com.adobe.ARM.[...].plist 3rd-Party support link
          [not loaded] com.google.GoogleContactSyncAgent.plist 3rd-Party support link
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          [not loaded] com.valvesoftware.steamclean.plist 3rd-Party support link
User Login Items:
          smcFanControl
          Dropbox
          NIHardwareAgent
          Fitbit Connect Menubar Helper
          DJM-900nexus AutoLauncher
          ProFire Agent
Internet Plug-ins:
          o1dbrowserplugin: Version: 5.2.4.18058 3rd-Party support link
          WacomNetscape: Version: 1.1.1-1 3rd-Party support link
          Unity Web Player: Version: UnityPlayer version 3.3.0f4 3rd-Party support link
          AdobeExManDetect: Version: AdobeExManDetect 1.1.0.0 - SDK 10.7 3rd-Party support link
          Flip4Mac WMV Plugin: Version: 2.4.4.2 3rd-Party support link
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          AdobePDFViewerNPAPI: Version: 10.1.9 3rd-Party support link
          FlashPlayer-10.6: Version: 12.0.0.77 - SDK 10.6 3rd-Party support link
          Silverlight: Version: 5.1.10411.0 - SDK 10.6 3rd-Party support link
          WacomTabletPlugin: Version: WacomTabletPlugin 2.0.0.4 3rd-Party support link
          Flash Player: Version: 12.0.0.77 - SDK 10.6 Outdated! Update
          iPhotoPhotocast: Version: 7.0 - SDK 10.8
          QuickTime Plugin: Version: 7.7.1
          googletalkbrowserplugin: Version: 5.2.4.18058 3rd-Party support link
          AdobePDFViewer: Version: 10.1.9 3rd-Party support link
          SharePointBrowserPlugin: Version: 14.0.0 3rd-Party support link
          JavaAppletPlugin: Version: Java 7 Update 51 3rd-Party support link
Safari Extensions:
          iGetter Extension: Version: 2.9.2
Audio Plug-ins:
          AirPlay: Version: 1.7 - SDK 10.8
          iSightAudio: Version: 7.7.1 - SDK 10.8
iTunes Plug-ins:
          Quartz Composer Visualizer: Version: 1.4 - SDK 10.8
User iTunes Plug-ins:
          SoundThing: Version: (null) 3rd-Party support link
          TrapcodeKlangfarbe_BETA5: Version: (null) 3rd-Party support link
User Internet Plug-ins:
          BlueStacks Install Detector: Version: 0.2.5 - SDK 10.6 3rd-Party support link
          iGetterScriptablePlugin: Version: 2.9.2 3rd-Party support link
          WebEx64: Version: 1.0 - SDK 10.5 3rd-Party support link
3rd Party Preference Panes:
          PenTablet 3rd-Party support link
          Cineform 3rd-Party support link
          Flash Player 3rd-Party support link
          Flip4Mac WMV 3rd-Party support link
          Java 3rd-Party support link
          PreferencesPane 3rd-Party support link
          MAudioMobilePreUSB 3rd-Party support link
          PreferencesPane 3rd-Party support link
          Perian 3rd-Party support link
          TechTool Protection 3rd-Party support link
Old Applications:
          InterLok Helper:          Version: 5.9 - SDK 10.4 3rd-Party support link
                    /Library/Application Support/PACE Anti-Piracy/InterLok Helper.app
          Uninstall Pro Tools:          Version: 10.0 - SDK 10.4 3rd-Party support link
                    /Applications/Avid/Pro Tools/Pro Tools Utilities/Uninstall Pro Tools.app
          Data Rescue 3:          Version: 3.2.1 - SDK 10.4 3rd-Party support link
          Angry Birds Rio:          Version: 1.0.0 - SDK 10.0 3rd-Party support link
          Audacity:          Version: 1.3.13.0 - SDK 10.4 3rd-Party support link
Time Machine:
          Skip System Files: NO
          Mobile backups: ON
          Auto backup: YES
          Volumes being backed up:
                    Macintosh HD: Disk size: 697.84 GB Disk used: 535.77 GB
          Destinations:
                    Time Machine [Network] (Last used)
                    Total size: 2
                    Total number of backups: 67
                    Oldest backup: 2013-04-27 22:06:51 +0000
                    Last backup: 2014-04-06 18:29:25 +0000
                    Size of backup disk: Adequate
                              Backup size 2 > (Disk used 535.77 GB X 3)
          Time Machine details may not be accurate.
          All volumes being backed up may not be listed.
Top Processes by CPU:
               5%          WindowServer
               2%          EtreCheck
               1%          Dropbox
               1%          Google Chrome
               1%          coreservicesd
Top Processes by Memory:
          233 MB          WebProcess
          176 MB          mds
          127 MB          Mail
          123 MB          Google Chrome
          90 MB          iTunes
Virtual Memory Information:
          236 MB          Free RAM
          1.58 GB          Active RAM
          1.23 GB          Inactive RAM
          723 MB          Wired RAM
          10.80 GB          Page-ins
          1.69 GB          Page-outs

I accidently put vr files in trash but did not delete, now stuck on grey screen after battery dying! Help

I am not very tech savvy but recently used a program that tells you what programs and files are using up large amounts of space on your computer I think it was called disc utility maybe. I deleted a whole bunch of things but accidently deleted a folder called vr, I realised I made a mistake and went to remove it from the trash when my laptop died, now it won't turn on past the grey screen with the apple logo!
I didn't delete the files they are just sitting in the trash. Is there anything I am able to do? I don't have any install discs or anything or wifi at my house or have any computer knowledge really. Please help!

Thank you! But do you think that a defective cable would cause it to not boot the cd now as well as the HD errors?
Also, this is kind of embarrassing, but if my trackpad happened to be broken to where I couldn't click it (broke a while back, but I use an external mouse so it never really bothered me) can I hold down the mouse button on my external mouse at startup to eject the cd or does it have to be the trackpad. If not, is there another way I can eject the cd?
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