Got a new hard drive, system now has very short freezes when being used

Hello there!
I recently got a new hard drive, 1 TB from 320, and i have been having an issue where the computer seems to freeze for about half a second and then go back to normal. This happens on multiple apps and accounts. i have had it happen in safari, firefox, Minecraft and warcraft 3. It seems to happen more when the system is under heavy use like if i am playing DvZ. Basically its like the display freezes and everything else keeps going. after about half a second or so the screen will jump to where it should be. This happens both in Minecraft and Warcraft 3. in safari it happens sometimes when i go back a page, it just kind of sits with the back button highlighted for a second then it goes to the previous page. Also sometimes when i scroll it takes a second or two to start scrolling.
The system itself is not freezing totally because stuff still happens when the screen is frozen, in Warcraft 3 units will jump to where they would be is the screen hadn't frozen.
I have tested it on multiple accounts so its not isolated to one account.
Thanks for any help you can give,
ZapplePi

Try booting into the Safe Mode using your normal account.  Disconnect all peripherals except those needed for the test. Shut down the computer and then power it back up after waiting 10 seconds. Immediately after hearing the startup chime, hold down the shift key and continue to hold it until the gray Apple icon and a progress bar appear. The boot up is significantly slower than normal. This will reset some caches, forces a directory check, and disables all startup and login items, among other things. When you reboot normally, the initial reboot may be slower than normal. If the system operates normally, there may be 3rd party applications which are causing a problem. Try deleting/disabling the third party applications after a restart by using the application un-installer. For each disable/delete, you will need to restart if you don't do them all at once.
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