Timing starts when you select Continue on your run file from the File Selection screen. Timing ends the frame the final cutscene starts at the end of the escape sequence.
To set up a run file, watch the intro of the game and then go back to the main menu. This will give you a file that skips the intro every time you do a run. Run files will normally say 00:03:44 in-game time (IGT), but a time barely higher or lower is still acceptable.
Any version is allowed.
Runs done on versions 1.0.0-1.0.2 are not allowed to use the Invincibility glitch, unless the run is being submitted to the Legacy board.
Runs done on versions pre-2.0.0 are unable to submit to Rookie/Dread Mode categories.
All submissions must be unique and not shared between multiple categories.