Ok so I sort of got it working. It does play through but its not perfect.
The issue arises when I click between skip intro and replay intro multiple times. Its unlikely to happen unless someone is testing the site but I'd like my site to perform as best as I can with my limited programming ability. I also want to avoid issues once I start adding content from the other pages. For testing, I created a version of each a TweenLite intro as well as a manually tweened version. The manual version always reloads perfectly when clicking around the site but the timing of the TweenLite version gets thrown off after a couple of replays in a row. I guess there would be programming fixes for this issue but im sure its beyond my ability.
Here's a short version of my modified TweenLite code. If you see anything that can would aid this issue let me know.. otherwise I'll sadly go with the manual version.
import com.greensock.*;
import com.greensock.easing.*;
import com.greensock.plugins.TweenPlugin;
import com.greensock.plugins.AutoAlphaPlugin;
TweenPlugin.activate([AutoAlphaPlugin]);
Slide_01._visible = false;
Slide_01._alpha = 0;
Slide_02._visible = false;
Slide_02._alpha = 0;
Slide_03._visible = false;
Slide_03._alpha = 0;
var timeline:TimelineLite = new TimelineLite();
timeline.append(TweenLite.to(Slide_01, 3, {autoAlpha:100, ease:Quad.easeIn}), 0);
timeline.append(TweenLite.to(Slide_02, 3, {autoAlpha:100, ease:Quad.easeIn}), 0);
timeline.append(TweenLite.to(Slide_03, 2, {autoAlpha:100, ease:Quad.easeIn}), -1.5);
//I have 20 extra slides following this sequence and below is the last line of code which automatically takes the intro to the main page.
TweenLite.delayedCall(62, _level0._root.gotoAndPlay, ["part1"], _level0);