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Have you tried resetting the PRAM. It goes a long way to fix hardware problems. My Pro was hanging almost every shutdown after installing 10.6 (sitting there with nothing but the desktop background and never shutting down). So I did the PRAM reset and it hasn't happened since.

Hold Command + Option + P + R until you here the bong a second time.
 
When you transferred data from the old drive to the new one, did you do it manually or use migration assistant?

Also, when you installed OS X on the new drive, was it working fine until you moved data over? If thats the case, there's clearly a software conflict. You might need to reinstall OS X again and then manually transfer files, reinstall apps etc.
 
You can also try a hardware test press n hold d with the install disk inside. Then it will come up with a report n stuff of anything that's wrong:)

You can also use carbon copy cloner which copies all your data. And makes the drive bootable hope this helps somewhat. And good luck:)
 
Thanks to everyone who has helped me, and I've finally resolved the issue.

Yesterday I installed smartsleep which allows you to control how your mac sleeps and I set it to sleep only, essentially disabling hibernation/safe sleep.

However I sometimes still had the issue when restarting, and the final thing I did that seems to have fixed everything was resetting the PRAM.

Again, thanks to everyone who posted, I appreciate it guys !
 
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