Have you tried using Toad Data Point to do the comparison?
Toad Data Point allows you to connect to 2 'systems' at the same time and do comparisons, reporting, transformations, profiling, etc., etc. The systems do not have to be the same, i.e. Oracle to Oracle. You can connect to virtually any data source, SqlServer, Excel, Access, Greenplum, DB2, Azure, Oracle, etc., etc. The list is long.
Heck, depending upon your data sources you may not need to connect to Oracle at all with this tool.
You can also save your query results to 'local storage' so you don't have to connect to a database to view the data after the initial connection and by using Toad Intelligence Central you can share the results of your queries, reports, files, etc., with other team members across the business.
I just wanted to share this idea with you since getting to data is what most of us want and we have a way to get it from multiple sources.
There is a lot of information on the ToadWorld site, under Toad Data Point, about the tool set.
-Mark