I created a movie clip that simulates handwriting that I placed into the first
frame of my main timeline. I put a stop action on the last frame of the movie
clip so it won't continuously loop, but now it won't play in my main timeline.
When I test the movie, it gets skipped over unless I rewind it, and then it
only plays the movie clip and not the rest of the movie. Geeze, I hope this
made sense as I need some help! This is driving me insane, and I am sure it is
something easy i overlooked...any help?

Without seeing the fla, it's hard to say, but I'm willing to bet that you have
a layer that you inserted a keyframe at the end of the timeline, and this is
where your stop(); is. If the layer in which your stop(); is doesn't have the
"dots" in each frame (i.e., blank spaces in between the beginning and end of
the timeline), then that stop happens right at the beginning of the timeline.
In any case, check all frames for stops.