As a test, I'd uninstall flash: Uninstall Flash Player | Windows
Then uninstall IE9 (going back to 8). Reboot.
If you system is fine without IE9 or flash, the next step would be to install Flash for IE8 and observe system performance again. If all is still ok, I'd uninstall the IE8 version of Flash and reboot. Now you are ready to install IE 9 again without trying to lay it on top of Flash. Reboot. Observe system performance with IE9 and no Flash for a while. Many of us are afraid of IE9 thanks to numerous posts of people having trouble with it or claimimg it's worse than IE8. But if your system is perfectly happy with it, your finally ready to add Flash to IE9 to see if that is the straw that broke the camel's back.
Also, take a look at posts #2 and #4 in this thread: IE9 issue