Have you gone through the BIOS and verified all of the settings are correct and disabled any hardware not used (such as serial ports, parallel port, etc.)? Flashing the BIOS results in everything being set to default, which should be fine, but there are sometimes issues.
Aside from that, try troubleshooting the problem. Watch the HDD LED when the slowness occurs to see if it is constantly on. Open Task Manager and watch the processes and cpu usage when the pause occurs. Check the Event Viewer in Windows and see if Windows is reporting any issues. Ensure you have all of the lastest drivers for your hardware. If Sony released a BIOS update, they likely released driver updates as well.