You correctly imply that this is somewhat easier in EG 4.1, but here are some instructions for EG 3.
To change the input table for a query in EG 3, follow these steps:
1. Add the new table you want to use into your project.
2. Right-click on the query, select Copy. Then right- click in the project view and select Paste. This should make a copy of your query definition.
3. Open your new copy of the query definition. In the query builder window, click on the Tables tab.
4. In the Tables view, right-click on the table that you want to change. Select "Change Table Location" from the context menu, and then select Project Data. A window with a list of project data sources appears.
5. Select the desired table from the list. Note that the table should have the same columns as your old table, at least as used by your query, to ensure that the query is still valid.
6. Click OK, and then run the query.
Note: you can change the table properties like this without first adding the table to your project, but when you do that the table reference is updated in the project, which I don't think you want. Your question sounds like you want to reuse your query definition for another table.
Chris