Why is it that when I test my game, the links of my previous decision are still open? Meaning I can go back and change a decision and it screws up the look of everything. Will that be in the final published version? And if so is there a way to remove it?

I don't really know about game books as I've only ever used Quest in Text Adventure mode. However, how pages are displayed can probably be tweaked in a similar manner. In the left pane click 'game' and then in the main window click 'display' and there's probably a box you need to check regarding clearing earlier options or clearing the screen or whatever. If that doesn't work I'll need to fire up Quest to try and work it out but that'd unlikely happen today.