First of all, there is no reason that this code should take up a block diagram this size. I'm guessing you inherited this code from another programmer but, upon first glance, this program looks like it could be shrunk down to fit on a 1024x768 screen without scrolling, if state machines, subVIs and event structures are used properly. It might be worth undertaking that task, if you are up for it and are willing to learn about proper program architecture. I'm sure you could get a lot of help from people on this forum if you decide to do that.
So is the code getting stuck in the first initialization loop with the dialogs about file locations and overwrite permissions, etc or somewhere else?