Ok, so let's do this one step at a time, leaving the patching til last. First, download Gamebooster:
http://iobit.com/downloadcenter.php?...ame-booster-v1 (direct link). It's the 1.6 version, there is a v.2 but it caused a few problems with my rig, dunno if it's just me but start with this one first as that's what I use. Click No when it asks if you want to update (when it starts up).
Once installed, restart the PC and immediately before you run SH3, run Gamebooster and click 'Gaming Mode'. It will bring up a dialog with a list of programs running on your PC *in addition* to the default processes it closes. Put a check in the boxes for any running programs you know you don't need during your game session then click 'Close them'. It should then close down all the checked processes and defrag and free up any RAM. It will then minimize itself to the tray and you can start SH3. See if that makes a difference first of all, if not, we'll start with the patches, but Gamebooster is good to have for any game so well worth having regardless.