I don't think you can overwrite DX9 with an older version... do this:
1. Create a Win98 boot disk if you don't already have one. I would assume that you know how to do this, but if not then tell me.
2. Boot from the floppy disk to get to a command prompt and type "scanreg/restore" without the quotes.
Hopefully there will be a registry backup listed that predates your excursion, which lasted for two weeks, right? Anyway, choose the oldest backup from the list, reboot, change boot priority to the hard drive, and see if it affected DirectX.
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