I use a program called Celtx to write my scripts. It really makes things easy. There are a few little bumps here and there, but nothing that cannot be easily dealt with.
I just spent the past hour or two re-working my Issue #1.
The main thrust of the story is unchanged, but I had to push things around a little bit in order to insert a few scenes that I needed to happen earlier in the story.
It also gave me a chance to go back in and correct some character names