Since the game has a built-in timer, that will be used when running individual levels.
Use the "puzzles only" to run individual levels. It appears that the boss stages cannot be done this way. So a good idea is to save before entering a boss stage to run in the full game to be able to rerun it indefinetly. For some reason the timer does not reset even if a stage is completed in a run, and therefore saving and reloading to re-run a boss stage starts where the timer finished. So to avoid having to play through the game to run the boss stage the timing will be counted from the beginning of the boss stage to the end time. For instance if the first number the timer shows is 8 min 25 sec and ends at 8 min 55 sec, the run is counted as a 30 sec run.
I will be adding individual levels whenever there is a run for it. Please just write me if you've done one not on the list yet, then i will add it.