Yes. You'll have to reinstall IE5.5 and MP7.
They're not included in Win98SE CD.

If you copy the files first to the HDD and then install Windows, you don't need to insert the installation CD when prompted. It'll copy the needed files directly from your drive.

I'd suggest a clean installation of Win98SE, if you want my opinion.
Sometimes there's trouble when you instal W98SE over W98.

Good luck.

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