I was having the same problems running SH3 on a notebook. I've recently found a program called 'Alacrity' (which you can get here alacritypc.com), which has made a huge difference.
Basically, you setup a profile for the game, and the idea is that it shuts everything down that's not needed (including the desktop etc), runs the game, then restarts everything automatically when you exit the game. Seems to work really well so far, and it's completely configurable.
The game doesn't look anywhere near as good on my notebook as some of the videos I've seen on YouTube (my notebook uses shared graphics), but it least it loads quicker, and runs a lot faster. Might be worth a try.
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