As always, guess-troubleshooting complex tech issues online depends on you providing absolutely as much info as possible - even that which you think is irrelevant.
Now actually, you've done better than most. So, let me get a couple little things out of the way first.
Extended is the format for your drive. Standard is less efficient and wastes space. It's only there because OS8 and below can't use extended. NOT your problem - it will actually work either way.
There were originally issues with 500MHz Yikes! boards and they were speed-dumped to 450 for a while. That is probably also
not your problem.
Remarkably, your SS-to SATA-to-ATA is probably OK as well. If it wasn't, it wouldn't work at all. Plus, you say you swapped them out without success.
You changed the optical drive. That ain't it either - same reason…it just wouldn't work.
You swapped the video card - also no fix.
All of that is what I mean by you've done better than most. At least you
had the other parts to replace and retry…imagine if you didn't!
You do have one problem: You went through everything 10 times. That's time you don't get back…

End of the day, the
real problem seems to be:
Mouse clicks don't work. You didn't say if keyboard commands DO work, so try this:
After you're at the desktop where you get stuck, try pressing ⌘N See if a new empty folder appears - If it does, immediately type a name for it. if that works, the keyboard is OK, the USB extension is enabled and working and the only problem left is……… THE MOUSE!
Now, reboot. After the chime, press and hold the shift key until you see the desktop and a little message "extensions off".
NOW see if the mouse works. If it does, you have an "extension conflict" If it doesn't,
are you certain the mouse is good? Is it an Apple mouse?Do you have another one of
those to try? I'm guessing no - if you did, you would have tried that already. Go beg, borrow or steal one.
If it's a 3rd-party mouse, you should try a different one even though it
should basically work. You may need a special extension for it.
Get this far and see if you can determine if, as I said, it's an "extension conflict" or a defective mouse, or a defective mouse or a fukin Gypsy curse and holler back.