Nice and detailed! I like this tutorial
Can't wait for part three. I wanted to wait till scripting was thoroughly covered to start messing with it. I'm having fun with this level editor so far 
If you see something in
underline, it means that it only works with 2.1.
X is a number, c is a color (giving arguments: cyan (

), purple and pink (

), blue (

), red (

), yellow (

) and green (

) (There is none for gray) and s is a script name.
say(x) - Create a text box with x lines. Text below the command will be the text.
say(x,c) -
Create a text box over crewmate c with x lines, and color c. Text below the command will be the text.say - Create a text box with 1 line. Text below the command will be the text.
reply(x) - Create a text box over

with x lines. This acts in the same way as say(x), only with the player's text box.
reply - Create a text box over

with x lines. This acts in the same way as say(x), only with the player's text box.
In 2.0, with say(x), say(x,c) and reply(x), you can have up to 5 lines. In 2.1 you can have 11.
music(x) - Play song x. The numbers are the same as in the main menu, and 0 for silence.
flash - Make the screen flash
happy - Makes

happy
sad - Makes

sad
happy(c) -
Makes crewmate c happysad(c) -
Makes crewmate c saddestroy(warptokens) - Destroy all warp tokens on the screen.
destroy(gravitylines) - Destroy all gravity lines on the screen. (It won't always work)
flag(x,on) Turns flag x on. There are flags 0-66 and 68-99.
flag(x,off) Turns flag x off.
ifflag(x,s) If flag x is on, go to script s.
iftrinkets(x,s) If you have at least x trinkets, go to script s.
map(on) -
Turns the map onmap(off) -
Turns the map offsqueak(c) -
Makes a crewmate squeaksqueak(on) -
Turns crewmate squeaking onsqueak(off) -
Turns crewmate squeaking offThat's all I know for now! Hope that helped!

P.S. There is no flag 67.