I use a free online tool called DeltaJSON from DeltaXML. It allows compare and merge, by analysing the structure rather than line by line, so is more effective for JSON files where the properties and values move around in the file. It can give a delta file to for the changes.
To automate the process you could write a script to retrieve the JSON files and then post them to the REST service they provide.
For a simple manual comparison you could use JSON Diff.