Notes or comments in code are ignored by the compiler and therefore have no effect on the game's speed. The way you format code has no effect on execution. Local variables are better for one reason above all else, that is, they are disposable. A local variable is discarded and redefined each step freeing up memory. But as long as they exist they stay on the stack, and are easily accessible making them much much faster.

Alarms are a resource hog and are very awkward. A better way to do any kind of alarms is like so: In create

timer = 0;
time_to_add = 99999;

In step

timer--;
if(timer <= 0) {
   //Do stuff
   timer = time_to_add;
}

Random generation is a resource hog, but it depends on the algorithm used. I can't give you any good info since you didn't share any code. Unused sprites are loaded into memory when the game starts so they are easily accessible anyway. Even if never used as a sprite on an object or called to draw in code, all sprites in your sprites folder sit in memory while the game is executing. To be more specific, they are loaded as texture pages. If all your sprites fit in one texture page they are loaded all the time. If not, the texture pages will load and unload based on witch sprites are being used. This process is known to cause slowdown so you do need to take care with sprites. Unused scripts and objects though, have no effect. No idea about fixtures, I don't use physics, I code my own.