Mac Mini REALLY won't sleep

OK, I have an Intel Mac Mini that really, REALLY won't sleep. When I try to sleep it, the heartbeat light on the front pulses, but I don't think the Mini is asleep, in that the external drives don't spin down (or they do spin down and then spin right back up again), and it wakes up too quickly. Also, when I try to use "Safe Sleep" ("pmset -a hibernatemode 1", or the Deep Sleep widget), the Mini doesn't deep sleep; it fakes normal sleep just like above (this used to work). I have tried all of the following:
1) Disconnecting all but a mouse and sleeping. Tried two different mice.
2) Resetting the SMU (15 minute unplug) and the NVRAM (CMD-OPT-P-R)
3) Booting from an external drive with a copy of a different Mini. Unmounted everything but the external drive first.
Is there anything else I should try?
Though I don't think it's relevant (due to point 3 above), the Mini has an internal drive with 2 partitions (a large Mac OS X partition in a RAID 1 with an external miniStack, and a small blank Boot Camp partition for a future XP install) and a miniStack with three partitions (the RAID mirror, a static backup, and a simple storage space). The hardware shouldn't be relevant due to point 2 above, but is a Ministack, a Logitech Marble Mouse, a Kenginston Orbit, an Apple Keyboard, a Dell 19" monitor with USB hub, a Griffin iMic, a Canon MP760, and an iSight.

Try downloading a copy of OnyX from
versiontracker.com...I find it solves almost
everything as it runs high level UNIX maintenance
scripts, such as Cron job, clearing kernel caches,
repairing permissions, etc.
Otherwise I'd try reset the PRAM by holding
Option-Cmd P, R at startup.
I had already tried Cmd-Opt-P-R. Disassembling the RAID and running MainMenu (similar to OnyX) fixed the problem. Seems the partition table may have been goobered somehow, because after I disassembled the RAID, Boot Camp wouldn't touch the drive (even though it supposedly had just an OSX partition and a Windows partition at that point).

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    com.tuxera.filesystems.tufsfs.fusefs_txantfs    2012.10.5
    com.vmware.kext.vmioplug.10.1.24    10.1.24
    com.vmware.kext.vmx86    0104.03.86
    com.vmware.kext.vmnet    0104.03.86
    com.vmware.kext.vsockets    90.4.23
    com.vmware.kext.vmci    90.4.18
    com.Cycling74.driver.Soundflower    1.6.6
    com.rogueamoeba.InstantOnCore    6.0.2
    com.rogueamoeba.InstantOn    6.0.2
    com.apple.iokit.SCSITaskUserClient    3.5.5
    com.apple.driver.AppleUSBCDC    4.1.23
    com.apple.filesystems.smbfs    1.8
    com.apple.driver.AppleBluetoothMultitouch    75.19
    com.apple.iokit.IOBluetoothSerialManager    4.1.3f3
    com.apple.filesystems.autofs    3.0
    com.apple.driver.X86PlatformShim    1.0.0
    com.apple.driver.AGPM    100.12.87
    com.apple.driver.ApplePlatformEnabler    2.0.6d1
    com.apple.driver.AppleMikeyHIDDriver    122
    com.apple.driver.AppleHDAHardwareConfigDriver    2.3.7fc4
    com.apple.driver.AppleHDA    2.3.7fc4
    com.apple.driver.AppleMikeyDriver    2.3.7fc4
    com.apple.driver.AppleMuxControl    3.3.0
    com.apple.driver.AppleUpstreamUserClient    3.5.10
    com.apple.driver.AppleMCCSControl    1.1.11
    com.apple.driver.AppleSMCPDRC    1.0.0
    com.apple.iokit.IOBluetoothUSBDFU    4.1.3f3
    com.apple.iokit.BroadcomBluetoothHCIControllerUSBTransport    4.1.3f3
    com.apple.driver.ACPI_SMC_PlatformPlugin    1.0.0
    com.apple.driver.AudioAUUC    1.60
    com.apple.iokit.IOUserEthernet    1.0.0d1
    com.apple.Dont_Steal_Mac_OS_X    7.0.0
    com.apple.driver.ApplePolicyControl    3.3.0
    com.apple.driver.AppleLPC    1.6.0
    com.apple.driver.AppleIntelHD4000Graphics    8.1.0
    com.apple.driver.AppleIntelFramebufferCapri    8.1.0
    com.apple.driver.AppleIRController    320.15
    com.apple.driver.AppleFileSystemDriver    3.0.1
    com.apple.AppleFSCompression.AppleFSCompressionTypeDataless    1.0.0d1
    com.apple.AppleFSCompression.AppleFSCompressionTypeZlib    1.0.0d1
    com.apple.BootCache    34
    com.apple.driver.XsanFilter    404
    com.apple.iokit.IOAHCIBlockStorage    2.3.1
    com.apple.driver.AirPort.Brcm4331    614.20.16
    com.apple.driver.AppleSDXC    1.4.0
    com.apple.iokit.AppleBCM5701Ethernet    3.6.0b1
    com.apple.driver.AppleFWOHCI    4.9.6
    com.apple.driver.AppleUSBHub    5.5.5
    com.apple.driver.AppleAHCIPort    2.5.1
    com.apple.driver.AppleUSBXHCI    5.5.5
    com.apple.driver.AppleUSBEHCI    5.5.0
    com.apple.driver.AppleEFINVRAM    1.7
    com.apple.driver.AppleRTC    1.5
    com.apple.driver.AppleACPIButtons    1.7
    com.apple.driver.AppleHPET    1.8
    com.apple.driver.AppleSMBIOS    1.9
    com.apple.driver.AppleACPIEC    1.7
    com.apple.driver.AppleAPIC    1.6
    com.apple.driver.AppleIntelCPUPowerManagementClient    196.0.0
    com.apple.nke.applicationfirewall    4.0.39
    com.apple.security.quarantine    2
    com.apple.driver.AppleIntelCPUPowerManagement    196.0.0
    com.apple.driver.AppleUSBMergeNub    5.5.5
    com.apple.iokit.IOSCSIBlockCommandsDevice    3.5.5
    com.apple.iokit.IOUSBMassStorageClass    3.5.1
    com.apple.driver.AppleBluetoothHIDKeyboard    170.2
    com.apple.driver.AppleHIDKeyboard    170.2
    com.apple.driver.IOBluetoothHIDDriver    4.1.3f3
    com.apple.driver.AppleMultitouchDriver    235.29
    com.apple.iokit.IOSerialFamily    10.0.6
    com.apple.kext.triggers    1.0
    com.apple.iokit.IOSCSIArchitectureModelFamily    3.5.5
    com.apple.driver.DspFuncLib    2.3.7fc4
    com.apple.driver.AppleBacklightExpert    1.0.4
    com.apple.driver.AppleSMBusPCI    1.0.11d0
    com.apple.driver.AppleSMBusController    1.0.11d0
    com.apple.driver.AppleThunderboltEDMSink    1.1.8
    com.apple.driver.AppleThunderboltEDMSource    1.1.8
    com.apple.driver.AppleThunderboltDPOutAdapter    1.8.9
    com.apple.iokit.IOFireWireIP    2.2.5
    com.apple.iokit.AppleBluetoothHCIControllerUSBTransport    4.1.3f3
    com.apple.driver.IOPlatformPluginLegacy    1.0.0
    com.apple.driver.X86PlatformPlugin    1.0.0
    com.apple.iokit.IOSurface    86.0.4
    com.apple.iokit.IOBluetoothFamily    4.1.3f3
    com.apple.iokit.IOAudioFamily    1.8.9fc11
    com.apple.kext.OSvKernDSPLib    1.6
    com.apple.driver.AppleSMC    3.1.4d2
    com.apple.driver.AppleGraphicsControl    3.3.0
    com.apple.driver.IOPlatformPluginFamily    5.3.0d51
    com.apple.driver.AppleHDAController    2.3.7fc4
    com.apple.iokit.IOHDAFamily    2.3.7fc4
    com.apple.iokit.IOAcceleratorFamily    30.14
    com.apple.iokit.IONDRVSupport    2.3.7
    com.apple.iokit.IOGraphicsFamily    2.3.7
    com.apple.driver.AppleThunderboltDPInAdapter    1.8.9
    com.apple.driver.AppleThunderboltDPAdapterFamily    1.8.9
    com.apple.driver.AppleThunderboltPCIDownAdapter    1.2.6
    com.apple.iokit.IOUSBHIDDriver    5.2.5
    com.apple.driver.AppleUSBComposite    5.2.5
    com.apple.driver.AppleThunderboltNHI    1.6.3
    com.apple.iokit.IOThunderboltFamily    2.2.6
    com.apple.iokit.IO80211Family    522.4
    com.apple.iokit.IOEthernetAVBController    1.0.2b1
    com.apple.iokit.IONetworkingFamily    3.0
    com.apple.iokit.IOFireWireFamily    4.5.5
    com.apple.iokit.IOAHCIFamily    2.3.1
    com.apple.iokit.IOUSBUserClient    5.5.5
    com.apple.iokit.IOUSBFamily    5.5.5
    com.apple.driver.AppleEFIRuntime    1.7
    com.apple.iokit.IOHIDFamily    1.8.1
    com.apple.iokit.IOSMBusFamily    1.1
    com.apple.security.sandbox    220.2
    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    1.7
    com.apple.iokit.IOPCIFamily    2.7.3
    com.apple.iokit.IOACPIFamily    1.4
    com.apple.kec.corecrypto    1.0
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    Memory Module: BANK 1/DIMM0, 4 GB, DDR3, 1600 MHz, 0x857F, 0x483634353155363446313630304700000000
    AirPort: spairport_wireless_card_type_airport_extreme (0x14E4, 0x10E), Broadcom BCM43xx 1.0 (5.106.98.100.16)
    Bluetooth: Version 4.1.3f3 11349, 2 service, 18 devices, 1 incoming serial ports
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    Serial ATA Device: M4-CT128M4SSD1, 128.04 GB
    USB Device: Generic USB Hub, 0x058f  (Alcor Micro, Corp.), 0x9254, 0x14300000 / 1
    USB Device: composite_device, 0x09a6  (Poinchips), 0x8001, 0x14310000 / 2
    USB Device: hub_device, 0x8087  (Intel Corporation), 0x0024, 0x1d100000 / 2
    USB Device: hub_device, 0x0424  (SMSC), 0x2512, 0x1d180000 / 3
    USB Device: IR Receiver, apple_vendor_id, 0x8242, 0x1d182000 / 5
    USB Device: BRCM20702 Hub, 0x0a5c  (Broadcom Corp.), 0x4500, 0x1d181000 / 4
    USB Device: Bluetooth USB Host Controller, apple_vendor_id, 0x828a, 0x1d181300 / 8
    USB Device: hub_device, 0x8087  (Intel Corporation), 0x0024, 0x1a100000 / 2
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    Dr. Smoke
    Author: Troubleshooting Mac® OS X

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    http://pastebin.com/raw.php?i=ZKUC3qWv

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