EB doesn't overwrite any of the files of vanilla RTW, meaning you could play EB and vanilla at the same time if you wanted to. So, you should be able to install it to the same folder RTR is installed to IF you used the modswitch version of RTR.
If you had the modswitch version of RTR, I bet you could just delete the RTR folder in your RTW folder and that's that. If you didn't use the modswitch version, you'd have to uninstall the entire thing, hopefully using the uninstall executable or through add/remove programs in your control panel. Then just manually delete all the other traces of the file, and you will have traces, and then install RTW once more.
I don't know why it stayed at 3 progress bars for an hour. I suggest you try again.
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