New hard drive, restored with time capsule -- safari won't open

Just successfuly replaced my crashed 500gb hard drive with a 2TB drive. Used time capsule to restore the system (what a godsend), but now programs on the computer arent working. I tunes opens, then crashes, the app store just bounces down in the application bar for a while then stops, safari opens 80% of a page and then the window crashes and goes away. I get a feeling it has something to do with my recent repairs, but what? Any help would be appreciated. this is very frustrating.
Original system is a white intel iMac 500GB 20 inch screen EMC# 2018.

ok, sorry for being new at this, but I just tried "repair disk" and have an almost infinite array of permissions errors....so many that it crashes when doing the repair. Is this a problem with the drive itself, or the fact that i restored an entire system onto a new drive? Either way, is it fixable?

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    Configure Time Machine preferences. Be sure to remove the external drive from the Exclude list.
    Mac Apps - Apple Support
    Mac Basics
    Welcome to Mac Support

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