Fan working overtime and jerky video

Around four days ago my MBP started getting really hot for no particular reason, I rebooted and all was well until I went on YouTube. Since then almost every time I watch a YouTube video in full screen, the video playback is jerky and the cooling fan kicks into overdrive. When I check activity monitor there aren't any processes using that much CPU power.
When the video goes jerky, the rest of the machine does too, until I close the video (or force quit the Flash plugin container). I have tried this on Firefox, Chrome and Safari, all yield the same results. I've re-installed Mountain Lion and Flash player (various versions, all the same result).
I then thought the issue might be hardware related, so I tried a different hard drive, different memory, cleaned out the fan and reset the SMC and PRAM more times than I can remember. Nothing is helping.
This is really bugging me, as it was working fine a few days ago, now I can't browse the Internet or make a Skype call (voice only) without the constant noise of the fan.

I would suggest trying to run an Apple hardware test using the disc supplied with your MBP
Intel-based Macs: Using Apple Hardware Test

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