Because the progress is tied to the amount of stamina blown at base, you can run whatever you want without worrying about efficiency, with one exception - The game only looks at original stamina cost. Because of this, the missions you want to run are going to be the ones that have cost deduction applied to it. Currently the 2 special missions do have a 50% reduction, so you're getting the credit of doing a 32 for the cost of 16. Otherwise I would point you towards doing the EX missions because the drop rates for high slot receptors is better there than anywhere else in the game.
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