This is rather simple..
You just gotta get the idea..
First things first. You have to make sure the map is behind the menu.
To do that, add this line:
@spriteset = Spriteset_Map.new
Preferably above the line: '#Make command window'
Now you have to make the windows see-through-able.
I'm only going to explain that for the first menu screen you see.
Find these lines:
@command_window = Window_Command.new(160, [s1, s2, s3, s4, s5, s6])
@command_window.index = @menu_index
...
# Make play time window
@playtime_window = Window_PlayTime.new
@playtime_window.x = 0
@playtime_window.y = 224
# Make steps window
@steps_window = Window_Steps.new
@steps_window.x = 0
@steps_window.y = 320
# Make gold window
@gold_window = Window_Gold.new
@gold_window.x = 0
@gold_window.y = 416
# Make status window
@status_window = Window_MenuStatus.new
@status_window.x = 160
@status_window.y = 0
Under every window, add the line:
@wtfkindofwindowisthisthatnameissupposedtobehere_window.opacity = 160 #(where 160 is the opacity)
It'll then look like this:
@command_window = Window_Command.new(160, [s1, s2, s3, s4, s5, s6])
@command_window.index = @menu_index
@command_window.opacity = 160
...
# Make play time window
@playtime_window = Window_PlayTime.new
@playtime_window.x = 0
@playtime_window.y = 224
@playtime_window.opacity = 160
# Make steps window
@steps_window = Window_Steps.new
@steps_window.x = 0
@steps_window.y = 320
@steps_window.opacity = 160
# Make gold window
@gold_window = Window_Gold.new
@gold_window.x = 0
@gold_window.y = 416
@gold_window.opacity = 160
# Make status window
@status_window = Window_MenuStatus.new
@status_window.x = 160
@status_window.y = 0
@status_window.opacity = 160
Now your menu is partly transparent!!
To also have the other menu-parts this way, repeat this for the windows in:
scene_item, scene_skill, scene_status.. and whatever scenes you got left..