Yeah, write a macro for excel, and have every spreadsheet run it. This macro will take the information you need and output it into a file in CSV format. Then using phpmyadmin just upload the CSV file. (CSV files are just plain text but have special format with commas seperating each field)
That's definitely the best way. To do it automatically, if you are running on a windows machine, you can use PHP to open up the COM object to control excel, and then simply loop through the whole list, systematically applying the macro.
Of course, the hard part to decide is this: all of this takes a bit of learning and research. You will need to get familiar (if your not already) with the excel macro language and possibly with PHP's COM extensions. Of course you'll have to debug all of this. 365 is actually not that much... it might be simpler to do it by hand. You can probably do the whole thing in less than a day, if you set up a good process. Like maybe, you could have one excel file open (with one sheet). Load up the old files about ten at a time. ANd simply copy paste the data into the new sheet in a logical way. Do this till all the required data is in the single sheet. In the next sheet, simply write an apropriate equation to copy all the data even nicer into a good format on the second sheet. Save the second sheet as CSV, and bingo you are done.