As a person who is more inclined to liking nice looking GUI, I feel the need to
do a revamp of the GUI further than what options are already customizable.
However not knowing a lick of coding I am perplexed as to where to start.

Would anyone be kind enough to help me out?

If you'd be kind enough to say how you'd like it changed.

Well, i'm looking to do the following:

Modify the style of the boxes.
Remove the direction box, or at least revamp it.
Rearrange the UI.
Change the overall style that the text and images are displayed.
Add more elements that will react based on flags.

Basically I want to make the end result look like something closer
to a java CYOA than just the basic QUEST5 one. Hopefully I can
also find a way to make it an SWF and publish the full thing to a
site like Kongregate.

The project is planned to be completed by years end and at current
moment most of the story sections have been written and planned
out as well as basic object, verb response and misc flavor text.

I think you are talking about the game gui not the editor gui? Most can be changed with css. Have a look at viewtopic.php?f=18&t=4410.