Gear Space

I have a 2000 YZ 125 and right before I took my bike apart I started to notice that when I shifted there was a little delay from when it would engage into the next gear. It wasn't alot but enough to notice. I needed a new top end, which I am replacing now, but this couldn't cause the gap could it? Any idea of how I can fix it would be greatly appreciated.
Also does anyone know how to decrease the space between 1st and 2nd gear. So I son't get caught in neutral.
Again thank you in advance.