Reformat & start again this time use an imaging program (listed below),create the first image after OS install,then another with a few of your most used apps,then another after a fully patched OS then add the rest of the 3rd party software starting from the most used to the least,obviously you won't want to so create one now actually make that two one time images,the time it takes to reformat & install the OS if you have an image you will have a fully operational updated OS ready to go in half the time now tell me how blown away you are
macrium reflect is free-create two sets of one time images on diff hdd's never rely on one in case of hdd failure or data corruption
ghost or acronis are paid
PS:images aren't affected by minor hardware changes like hdd,dvd,graphic card etc,mobo on the other hand might stuff em up a bit