I am not familiar with the multiple connections VBO but you should be able to use the Data - OLEDB VBO with single connection to do a join between the 2 files. You can set up the connection to your new file then in the SQL query you can do a join on to the prior file specifying the connection details in the query.
Query should look something like this
"""
SELECT t1.[key], (t1.[value] - t2.[value]) AS [Diff Of Values] FROM [1st_Excel_sheet_name$A:B] as t1 INNER JOIN [Excel 12.0 Xml;HDR=Yes;Database=path_to_2nd_excel].[2nd_Excel_sheet_name$A:B] as t2 ON t1.[key] = t2.[key]
"""
Obviously just replace with the details of your actual excel files, (file paths, sheet names and column names). If you only need to look at data in the current file then I think a LEFT JOIN would work, example is for INNER JOIN. If you need an OUTER JOIN then you would need to do a LEFT and RIGHT join separately then combine and remove duplicates (if I am remembering correctly).
