You shoudl not uninstall a thing. And the 1.29f patch shall be left
(if you reinstall you do best in doing it as follows:
1. Install Civ3
2. Install Civ3 1.29f patch
3. Install PTW
4. Install the latest PTW patch
)
You should not reinstall any civ3 patch after the PTW patch (even thou it dosn't afferct anything as Civ3 still can be run indepent of that PTW is installed. However PTW uses graphic files from Civ3 to run)