Hi Ed,
The uninstallation of XModIDE does not fully uninstall XModIDE in DNN4 due to limitation in the installer (unability to delete page). When uninstalling the IDE, you will have to manually delete the launch page from under the Admin Tab.
As for upgrade, what is changing between the DNN4 and DNN5 version of XModIDE is only the main dll (Adequation.DNNModules.XModIDE). After upgrading to DNN5, you should be able to overwrite this dll under /bin with the one from the DNN5 package.
The other approach is what you have done. Uninstall the DNN4 version, delete the launch page under admin, install the DNN5 version.
Let us know how it goes from there.