1 - This is where your problem lies, extra processes includes real-time virus scanning of memory and files as they are opened. So check with both FileMonitor and ProcessMonitor to see what is taking up those cpu cycles. I found by shutting of real time protection, my system started behaving normally again. And I lose no protection.
2 - WindowBlinds and ObjectDock are great and run incredibly fast, faster than the GDI that comes with XP, this isn't your problem.
3 - Partitions have no bearing unless you have a horribly slow drive with no caching and are doing strange things with swap drives, things you would already know to be performance sappers.
4 - Components age and fail eventually, drop a few Mhz and see what happens. Also, in the name of stability and compatibility later drivers of various components are not as OC friendly as earlier versions...this is especially true for games and video card drivers...what you can reach in Mhz with one game and one driver revision does not guarantee you can reach that same Mhz with a different driver version, or a different game.
The AMD DC Optimizer is mostly for out of API stuff, like video codecs, Bink, cut-scenes, things of that nature. Your best bet is to have the latest CPU driver, a finely tuned bios including the lowest RAM latencies possible and the /usepmtimer switch.
After you have thoroughly scoured your system for cpu sapping applets and if you find a specific game skips or acts very peculiar with the /usepmtimer switch on, take it out and see if that fixes it. Since the number of games that will break with /usepmtimer on is less than the number of games it fixes, resulting in a net gain. Also you avoid having that AMD TSR haunting you in your tray. But you are correct, properly threaded games don't need the pmtimer fix.