Finder doesn't open folders/preview apps gone missing

So i was sorting through my gazillion of photos last night and decided to also delete some photo editing programs i do not use at the moment to have some more space on my 3 year old macbook for the time being, and using CleanMyMac app, i removed aperture 3 and lightroom2 and lightroom 3Beta. I dont know what happened but my preview app doesnt want to work anymore and quickview doesnt show previews as it did, ie only thumbnails of JPGs. I restarted the system only to find out that now even the folders images dont show, only the names underneath. And i cannot open them either. I tried opening iPhoto, but it said that it aborted as the image could not be found. Using Bridge i amanged to get into the folders and everything is still there safe and sound. Only my Apps are not there, image wise, but kinda are. And funny enough it affected skype - no text is showing in the msg window.
I ran permission verification with some warnings and disk verification didnt complete vecause there were some number of.. not sure what it was... not matching. I just tried running it again to give exact details but i cannot find disk utility?!!?!?!?! doesn't come up in spotlight.
What did i do wrong?! What do i do?! PLS PLS help.
THANK YOU SO MUCH

Hi,
Thank you for the informative process to help. I just tried all of the above. My HD doesnt give error messages anymore and has been fixed, however the issue still persists.
When running permission repair i got a lot of messages. sorry for the long message but here is what it said. I am sharing because it means close to nothing to me.
Repairing permissions for “Macintosh HD”
Reading permissions database.
Reading the permissions database can take several minutes.
Permissions differ on "Library/Application Support/ProApps/Internal Plug-Ins/BrowserKit/iLife.bkplugin/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Permissions differ on "System/Library/PrivateFrameworks/BrowserKit.framework/Versions/A/CodeResources ", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/DVD.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSettings.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/FRSources.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Movies.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Music.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Photos.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/Podcasts.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/CoreServices/Front Row.app/Contents/PlugIns/TV.frappliance/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/BackRow.framework/Versions/A/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
Permissions differ on "System/Library/PrivateFrameworks/ProKit.framework/Versions/A/Resources/Leopard Panels.bundle/Contents/CodeResources", should be -rw-r--r-- , they are lrw-r--r-- .
ACL found but not expected on "usr/share/man/man3/ConfigWind.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/MoveToplev.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_ChangeWindowAttributes.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_ConfigureWindow.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_DefineCursor.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_MoveResizeWindow.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_MoveToplevelWindow.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_MoveWindow.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_ResizeWindow.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_SetWindowBackground.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_SetWindowBackgroundPixmap.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_SetWindowBorder.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_SetWindowBorderPixmap.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_SetWindowBorderWidth.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_SetWindowColormap.3tcl.gz".
ACL found but not expected on "usr/share/man/man3/Tk_UndefineCursor.3tcl.gz".
Warning: SUID file "Applications/Utilities/ODBC Administrator.app/Contents/Resources/iodbcadmintool" has been modified and will not be repaired.
Warning: SUID file "Applications/System Preferences.app/Contents/Resources/installAssistant" has been modified and will not be repaired.
Warning: SUID file "Applications/Utilities/Keychain Access.app/Contents/Resources/kcproxy" has been modified and will not be repaired.
Warning: SUID file "System/Library/PrivateFrameworks/DiskManagement.framework/Versions/A/Resources /DiskManagementTool" has been modified and will not be repaired.
Permissions differ on "Library/QuickLook/iWork.qlgenerator/Contents/CodeResources", should be -rw-rw-r-- , they are lrw-rw-r-- .
Warning: SUID file "usr/sbin/pppd" has been modified and will not be repaired.
Warning: SUID file "usr/sbin/vpnd" has been modified and will not be repaired.
ACL found but not expected on "Applications/Utilities".
Permissions repair complete
THANK YOU

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