Writing data to an Excel sheet using openpyxl
Perhaps manipulating data in the spreadsheet is not the most efficient way to do this, could you save the spreadsheet as a csv, and then you could read both spreadsheets into a list structure using the python core csv module.

Alternatively, you might use the Pandas library to import the csv files to a dataframe, do your processing and resave to a csv output. 

You can write your results out as csv, open this in excel and resave as an xlxs file.

Both of these approaches should take a few seconds to run