So, I managed to fix the permissions on the drives. I think the problem now is many of my system files have permissions errors which disk utility is not fixing. Also, all my drives still show up as external. Here is a console read from when i boot up:
10/30/10 9:55:02 AM com.apple.launchctl.LoginWindow[92] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/at.obdev.LittleSnitchNetworkMonitor.plist
10/30/10 9:55:02 AM com.apple.launchctl.LoginWindow[92] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/at.obdev.LittleSnitchUIAgent.plist
10/30/10 9:55:02 AM com.apple.launchctl.LoginWindow[92] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/com.razer.DeathAdder.Daemon.plist
10/30/10 9:55:02 AM com.apple.launchctl.LoginWindow[92] launchctl: Dubious permissions on file (skipping): /System/Library/LaunchAgents/com.apple.AirPortBaseStationAgent.plist
10/30/10 9:55:03 AM blued[65] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM loginwindow[54] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.544 loginwindow[54:107] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.launchctl.Background[102] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/at.obdev.LittleSnitchNetworkMonitor.plist
10/30/10 9:55:03 AM com.apple.launchctl.Background[102] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/at.obdev.LittleSnitchUIAgent.plist
10/30/10 9:55:03 AM com.apple.launchctl.Background[102] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/com.razer.DeathAdder.Daemon.plist
10/30/10 9:55:03 AM com.apple.launchctl.Background[102] launchctl: Dubious permissions on file (skipping): /System/Library/LaunchAgents/com.apple.AirPortBaseStationAgent.plist
10/30/10 9:55:03 AM com.apple.launchctl.Aqua[103] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/at.obdev.LittleSnitchNetworkMonitor.plist
10/30/10 9:55:03 AM com.apple.launchctl.Aqua[103] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/at.obdev.LittleSnitchUIAgent.plist
10/30/10 9:55:03 AM com.apple.launchctl.Aqua[103] launchctl: Dubious permissions on file (skipping): /Library/LaunchAgents/com.razer.DeathAdder.Daemon.plist
10/30/10 9:55:03 AM com.apple.launchctl.Aqua[103] launchctl: Dubious permissions on file (skipping): /System/Library/LaunchAgents/com.apple.AirPortBaseStationAgent.plist
10/30/10 9:55:03 AM com.apple.launchd.peruser.501[101] (com.apple.ReportCrash) Falling back to default Mach exception handler. Could not find: com.apple.ReportCrash.Self
10/30/10 9:55:03 AM UserAccountUpdater[104] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.660 UserAccountUpdater[104:903] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM compatchecker[105] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.812 compatchecker[105:903] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM lsregister[107] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.coreservicesd[75] 2010-10-30 09:55:03.903 lsregister[107:903] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM migCacheCleanup[108] Flushing Cache Locations...
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.980 migCacheCleanup[108:903] Flushing Cache Locations...
10/30/10 9:55:03 AM migCacheCleanup[108] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.990 migCacheCleanup[108:903] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.994 loginwindow[54:107] Error loading /Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio: dlopen(/Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio, 262): no suitable image found. Did find:
10/30/10 9:55:03 AM loginwindow[54] Error loading /Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio: dlopen(/Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio, 262): no suitable image found. Did find:
/Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio: no matching architecture in universal wrapper
10/30/10 9:55:03 AM com.apple.loginwindow[54] /Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio: no matching architecture in universal wrapper
10/30/10 9:55:03 AM loginwindow[54] Cannot find function pointer NewPlugIn for factory C5A4CE5B-0BB8-11D8-9D75-0003939615B6 in CFBundle/CFPlugIn 0x109902c60 </Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin> (bundle, not loaded)
10/30/10 9:55:03 AM com.apple.loginwindow[54] 2010-10-30 09:55:03.995 loginwindow[54:107] Cannot find function pointer NewPlugIn for factory C5A4CE5B-0BB8-11D8-9D75-0003939615B6 in CFBundle/CFPlugIn 0x109902c60 </Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin> (bundle, not loaded)
10/30/10 9:55:04 AM Dock[110] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:04 AM activateSettings[114] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:04 AM SystemUIServer[111] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:04 AM fontd[115] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:04 AM fontworker[125] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:04 AM Finder[112] CFPreferences: user home directory at
file://localhost/Users/Nick/ is unavailable. User domains will be volatile.
10/30/10 9:55:05 AM SystemUIServer[111] Error loading /Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio: dlopen(/Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio, 262): no suitable image found. Did find:
/Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin/Contents/MacOS/DVCPROHDAudio: no matching architecture in universal wrapper
10/30/10 9:55:05 AM SystemUIServer[111] Cannot find function pointer NewPlugIn for factory C5A4CE5B-0BB8-11D8-9D75-0003939615B6 in CFBundle/CFPlugIn 0x11b404720 </Library/Audio/Plug-Ins/HAL/DVCPROHDAudio.plugin> (bundle, not loaded)