Minecraft Checkpoint Commands

Go to the location where you want new players to spawn in, make sure there are no blocks above you (you should be able to look straight up and see the sky).
	/weather clear 999999
	/scoreboard objectives add checkpoint dummy
	/setworldspawn (remember the coordinates you do this at)
	/gamerule spawnRadius 0
	/gamerule keepInventory True

Starter command block: This should be next to your worldspawn, it's for players who are first joining. Put in a commandblock connected to a button.
	Grey button settings: Impulse : Unconditional : Needs Redstone
	/scoreboard players set @a[r=5] checkpoint 0

Then you should have these command blocks near your spawn. They give the player a "reset potion" to drink if they fall (and be teleported to their last checkpoint). You have to fill in the all caps parts with the coordinates of the place where you used /setworldspawn.
	Grey button settings: Repeat : Unconditional : Always Active
	/testfor @a[x=WORLDSPAWN-X,y=WORLDSPAWN-Y,z=WORLDSPAWN-Z,r=4,score_checkpoint_min=0]
	Grey button settings: Chain : Conditional : Always Active
	/replaceitem entity @a[x=WORLDSPAWN-X,y=WORLDSPAWN-Y,z=WORLDSPAWN-Z,r=4,score_checkpoint_min=0] slot.hotbar.7 minecraft:potion 1 0 {CustomPotionEffects:[{Id:7,Amplifier:10,Duration:20}]}

Checkpoints. For every checkpoint you have, you'll need one of these. Attach them as chain command blocks to the "reset potion" chain. You have to fill in the all caps parts with the coordinates and sequence number of each individual checkpoint. The first checkpoint (number zero) is the starting location of the parkour.
	Grey button settings: Chain : Unconditional : Always Active
	tp @a[x=WORLDSPAWN-X,y=WORLDSPAWN-Y,z=WORLDSPAWN-Z,r=4,score_checkpoint_min=CHECKPOINT-NUMBER,score_checkpoint=CHECKPOINT-NUMBER] CHECKPOINT-X CHECKPOINT-Y CHECKPOINT-Z

Then have one of these commands at every checkpoint (Except the first one).
	Grey button settings: Repeat : Unconditional : Always Active
	scoreboard players set @a[r=4] checkpoint CHECKPOINT-NUMBER

Optional repeating command that make players never run out of food.
	Grey button settings: Repeat : Unconditional : Always Active
	/effect @a minecraft:saturation 1 0 true