When does the game end when the last player pushes the first player over the 40-point limit?
The game ends immediately after someone has 40+ intel points. You must have a different version of the rulebook. The copy on the playtheagents website states twice:

The Goal - Your goal is simple - to be the first player to reach 40 intel points.
Reminder: the first person to reach 40 intel points, wins.

There is no mention of ending the game only on a players turn when they have 40+ intel points, nor requiring all players to have the same number of turns.