I don't have an official tally (not sure there is one) but you should definitely not add these numbers up. Most people working for the Commission, the Parliament, and the Council are EU civil servants and included in the 55000 figure. Some of them are not and yet the sum of the numbers you found for the Commission, the Parliament and the Council is less than 55000 but that's to be expected as some EU civil servants work for smaller institutions (the Court, the European Central Bank, etc.) and for specialised agencies.
Now, for the Commission (not the whole EU), this document released by the Directorate-General for Human Resources and Security indicates that roughly 20000 people (out of the 33000 working there) are civil servants (counted as Official AD, Official AST and Official AST/SC in the chart). The rest are temporary employees, contractors (especially for support functions like IT), national civil servants or experts (e.g. référendaires at the Court of Justice are not required to be civil servants, which gives judges complete freedom to hire whoever they want).
Assuming the ratio is the same across all other institutions and agencies (not sure how reasonable this is), this would work out to around 90000 people working for the European Union.