Whenever I make a very long conversation tree it always turns into a mess where it condenses to the point where I can't even input anything new. It always ends up like this even after stretching the window to its max:

Is there a better way to do this for longer conversations so the GUI can handle it?

As a note, I have used the "pop out" feature but at a certain point quest just crashes and I can't prevent it.

I would suggest splitting it up by using functions in these cases. I name the functions according to the NPC/object and topic / action, like "bob_c_weather", "bob_c_tragic_childhood", ... (and I use the c as and indicator for conversations). You may also try to use the codeview in cases where you can still manage it without using functions.

And for conversations especially I suggest to take a look at the ConversationLibrary:
https://github.com/ThePix/quest/wiki/Library:-Conversations

With that I am able to easily handle longer and more complex conversations.

This is fabulous! Thank you so much! The function worked out really well but I'm also going to look over this conversation library!