Mac pro 2008 problems

I'm having problems with my Mac Pro 2 x 3.2 GHz Quad-Core Intel Xeon ,early 2008 model. It still works fast enough for all my apps, running CS6. Issues are
Software hanging, pen drives not showing in the finder sometimes, issues with CD drive too. A ? over startup drive.
I'm constantly having to shut it down with the power button, and to reboot. It rarely restarts properly.
I'm on Yosemite, and can't update iphoto. I have intermitent problems with itunes, its not finding iphones when plugged in?
Is there a fix it that I can download from the internet to fix all these bugging issues, details of my system below. Help please?
Model Name:    Mac Pro
Model Identifier:    MacPro3,1
Processor Name:    Quad-Core Intel Xeon
Processor Speed:    3.2 GHz
Number of Processors:    2
Total Number of Cores:    8
L2 Cache (per Processor):    12 MB
Memory:    12 GB
Bus Speed:    1.6 GHz
Boot ROM Version:    MP31.006C.B05

Get a new system SSD boot drive. Do a clean install. Be careful what you import. SSD will give your system some juice.
Clone your system with Carbon Copy Cloner and enable the hidden advanced preference option - custom clone feature - to do a checksum on all files copied.
From your description, you should be doing both a SAFE BOOT and Recovery Mode to Repair Disk to fix the disk directory. Zap the PRAM from cold start and reset the STARTUP DISK setting.
I would not trust or rely on that drive and system as is for now.
Another, never use an unstable drive to install, or write to, should be using a backup spare system at this point.
Co clone it to SSD with CCC - after using DU and Safe Boot, and uninstalling any "non-essential" 3rd party app or background process and utilities. Lean, mean, stable and faster performance without the extras.
CS6: I would go for more RAM . FBDIMMs are downright affordable, look for NEMIX on Amazon while looking for Samsung 850 or Samsung XP941. Two: one for system, one for scratch, would be ideal. An EVGA 960 GTX to provide CUDA to CS6 maybe later or 970, more VRAM  the better.

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    Interval Since Last Panic Report:  122463 sec
    Panics Since Last Report:          1
    Anonymous UUID:                    52E60929-F5AE-D9CD-04B0-1872526C0821
    Mon Oct 13 10:58:17 2014
    panic(cpu 3 caller 0xffffff8007cb8945): Kernel trap at 0xffffff8007ef69e0, type 14=page fault, registers:
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    RAX: 0xffffff80209bb7e8, RBX: 0xffffff801fc6d808, RCX: 0x0000000009000000, RDX: 0xffffff801fc6dde0
    RSP: 0xffffff8131b7bbc0, RBP: 0xffffff8131b7bc00, RSI: 0x00000000000c43ff, RDI: 0xffffff801fc6dde0
    R8:  0x0000000000000000, R9:  0x0000000000000000, R10: 0xffffff80220fbfa4, R11: 0x0000000000000020
    R12: 0xffffff801fc6dde0, R13: 0x00000000000c43ff, R14: 0x00000000000c43ff, R15: 0x0000000000000002
    RFL: 0x0000000000010202, RIP: 0xffffff8007ef69e0, CS:  0x0000000000000008, SS:  0x0000000000000010
    Fault CR2: 0x000000000000008a, Error code: 0x0000000000000000, Fault CPU: 0x3
    Backtrace (CPU 3), Frame : Return Address
    0xffffff8131b7b860 : 0xffffff8007c1d636
    0xffffff8131b7b8d0 : 0xffffff8007cb8945
    0xffffff8131b7baa0 : 0xffffff8007ccebfd
    0xffffff8131b7bac0 : 0xffffff8007ef69e0
    0xffffff8131b7bc00 : 0xffffff8007eee0d6
    0xffffff8131b7be00 : 0xffffff8007d1a5d6
    0xffffff8131b7be60 : 0xffffff8007d092aa
    0xffffff8131b7bf50 : 0xffffff8007fe97ba
    0xffffff8131b7bfb0 : 0xffffff8007ccf453
    BSD process name corresponding to current thread: mdworker
    Mac OS version:
    12F45
    Kernel version:
    Darwin Kernel Version 12.5.0: Sun Sep 29 13:33:47 PDT 2013; root:xnu-2050.48.12~1/RELEASE_X86_64
    Kernel UUID: EA38B02E-2B88-309F-BA68-1DE29F605DD8
    Kernel slide:     0x0000000007a00000
    Kernel text base: 0xffffff8007c00000
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    com.apple.iokit.IOSurface 86.0.4
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    com.apple.iokit.IOUSBUserClient 630.4.4
    com.apple.iokit.IOFireWireFamily 4.5.5
    com.apple.iokit.IOAHCIFamily 2.5.1
    com.apple.iokit.IONetworkingFamily 3.0
    com.apple.iokit.IOATAFamily 2.5.1
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    com.apple.driver.AppleEFIRuntime 2.0
    com.apple.iokit.IOSMBusFamily 1.1
    com.apple.security.sandbox 220.3
    com.apple.kext.AppleMatch 1.0.0d1
    com.apple.security.TMSafetyNet 7
    com.apple.driver.DiskImages 345
    com.apple.iokit.IOStorageFamily 1.8
    com.apple.driver.AppleKeyStore 28.21
    com.apple.driver.AppleACPIPlatform 1.8
    com.apple.iokit.IOPCIFamily 2.8
    com.apple.iokit.IOACPIFamily 1.4
    com.apple.kec.corecrypto 1.0
    Model: MacPro3,1, BootROM MP31.006C.B05, 8 processors, Quad-Core Intel Xeon, 2.8 GHz, 10 GB, SMC 1.25f4
    Graphics: ATI Radeon HD 2600 XT, ATI Radeon HD 2600, PCIe, 256 MB
    Memory Module: DIMM Riser B/DIMM 1, 2 GB, DDR2 FB-DIMM, 800 MHz, 0x02FE, 0x47523244463247425838454C3830304E3252
    Memory Module: DIMM Riser B/DIMM 2, 2 GB, DDR2 FB-DIMM, 800 MHz, 0x02FE, 0x47523244463247425838454C3830304E3252
    Memory Module: DIMM Riser A/DIMM 1, 1 GB, DDR2 FB-DIMM, 800 MHz, 0x80AD, 0x48594D5035313241373243503844332D5335
    Memory Module: DIMM Riser A/DIMM 2, 1 GB, DDR2 FB-DIMM, 800 MHz, 0x80AD, 0x48594D5035313241373243503844332D5335
    Memory Module: DIMM Riser A/DIMM 3, 2 GB, DDR2 FB-DIMM, 800 MHz, 0x02FE, 0x47523244463247425838454C3830304E3252
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    PCI Card: ATI Radeon HD 2600, sppci_displaycontroller, Slot-1
    Serial ATA Device: Samsung SSD 840 PRO Series, 512,11 GB
    Serial ATA Device: ST31000524AS, 1 TB
    Parallel ATA Device: PIONEER DVD-RW  DVR-112D
    USB Device: hub_device, apple_vendor_id, 0x9120, 0xfd500000 / 2
    USB Device: Keyboard Hub, apple_vendor_id, 0x1006, 0xfd520000 / 4
    USB Device: Apple Optical USB Mouse, apple_vendor_id, 0x0304, 0xfd521000 / 6
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    EtreCheck version : 2.0.2 (86)
    Rapport créé 13 octobre 2014 11:23:31 UTC+02:00
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      Mac Pro (début 2008)
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      DIMM Riser B/DIMM 1
      2 GB DDR2 FB-DIMM 800 MHz ok
      DIMM Riser B/DIMM 2
      2 GB DDR2 FB-DIMM 800 MHz ok
      DIMM Riser A/DIMM 1
      1 GB DDR2 FB-DIMM 800 MHz ok
      DIMM Riser A/DIMM 2
      1 GB DDR2 FB-DIMM 800 MHz ok
      DIMM Riser B/DIMM 3
      empty empty empty empty
      DIMM Riser B/DIMM 4
      empty empty empty empty
      DIMM Riser A/DIMM 3
      2 GB DDR2 FB-DIMM 800 MHz ok
      DIMM Riser A/DIMM 4
      2 GB DDR2 FB-DIMM 800 MHz ok
      Bluetooth: Vieux - Handoff/Airdrop2 pas disponible
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      ATI Radeon HD 2600 - VRAM : 256 MB
      Cinema HD Display 2560 x 1600
    Logiciel du système : ℹ️
      OS X 10.8.5 (12F45) - Uptime: un jour 0:11:6
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      Samsung SSD 840 PRO Series disk0 : (512,11 GB)
      Statut S.M.A.R.T. : Vérifié
      disk0s1 (disk0s1) <non monté>  : 210 Mo
      MacPro SSD (disk0s2) /  [Startup] : 511.25 Go (472.61 Go libre)
      Recovery HD (disk0s3) <non monté>  [Restauration] : 650 Mo
      ST31000524AS disk1 : (1 TB)
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      disk1s1 (disk1s1) <non monté>  : 210 Mo
      MacPro 1To (disk1s2) /Volumes/MacPro 1To  : 999.35 Go (633.08 Go libre)
      Recovery HD (disk1s3) <non monté>  [Restauration] : 650 Mo
    Informations USB : ℹ️
      Verbatim Portable USB Drive 320,07 GB
      Statut S.M.A.R.T. : Vérifié
      disk3s1 (disk3s1) <non monté>  : 210 Mo
      320 Go Christophe Syren (disk3s2) /Volumes/320 Go Christophe Syren  : 319.73 Go (313.64 Go libre)
      USB 2.0 USB Flash Drive 8,17 GB
      Statut S.M.A.R.T. : Vérifié
      SANS TITRE (disk2s1) <non monté>  : 8.17 Go
      Apple, Inc. Keyboard Hub
      Mitsumi Electric Apple Optical USB Mouse
      Apple, Inc Apple Keyboard
      Apple Inc. Bluetooth USB Host Controller
    Gatekeeper : ℹ️
      Mac App Store et développeurs identifiés
    Représentants de lancement : ℹ️
      [désengagé] com.adobe.AAM.Updater-1.0.plist Aide
      [désengagé] com.adobe.CS5ServiceManager.plist Aide
      [désengagé] com.extensis.FMCore.plist Aide
    Daemons de lancements : ℹ️
      [invalid?] com.adobe.SwitchBoard.plist Aide
    Représentants de lancement pour l’utilisateur : ℹ️
      [désengagé] com.adobe.AAM.Updater-1.0.plist Aide
      [désengagé] com.adobe.ARM.[...].plist Aide
    Éléments Ouverture : ℹ️
      iTunesHelper Application (/Applications/iTunes.app/Contents/MacOS/iTunesHelper.app)
      Dropbox Application (/Applications/Dropbox.app)
    Plug-ins internet : ℹ️
      OfficeLiveBrowserPlugin : Version : 12.3.6 Aide
      AdobePDFViewer : Version : 9.5.5 Aide
      QuickTime Plugin : Version : 7.7.1
      JavaAppletPlugin : Version : 14.9.0 - SDK 10.7 Vérifier la version
    Panneaux de préférences de 3ème partie : ℹ️
      Growl  Aide
    Time Machine : ℹ️
      Skip System Files: NO
      Sauvegarde automatique : OUI
      Disques sauvegardés :
      MacPro SSD : Taille de disque : 511.25 Go Disque utilisé : 38.64 Go
      Destinations :
      Data [Network]
      Taille totale : 2 To
      Nombre de sauvegardes total : 9
      Sauvegardes la plus agée : 2014-10-08 01:39:21 +0000
      Dernière sauvegarde : 2014-10-10 11:31:35 +0000
      Taille de la disque de sauvegarde : Excellent
      Taille de sauvegarde 2 To > (Taille de disque 511.25 Go X 3)
    L’utilisation du CPU par processus : ℹ️
          1% WindowServer
          0% ps
          0% fontd
          0% System Events
          0% coreservicesd
    L’utilisation de la mémoire par processus : ℹ️
      97 Mo Dock
      97 Mo Finder
      75 Mo WindowServer
      64 Mo com.apple.security.pboxd
      64 Mo CalendarAgent
    Informations de la mémoire virtuelle : ℹ️
      523 Mo RAM Disponible
      1.04 Go RAM Active
      307 Mo RAM Inactive
      8.86 Go RAM Résidente
      266 Mo Pages entrants
      0 o Sorties pages

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