Engine fusebox removal and/or replacement

Hi! I'm not shure if this topic is covered somewhere else, if so I'm sorry for any double posting. 

First of all let me introduce myself. 31year old Norwegian who love cars and motorcycles. I have done mechanical and electrical work on all my previous cars, but these where from the "good old days" (Classic Mini, Volvo Duett (65), Opel Kadett (68) and my Honda CB500four (73)) and trying to get a grasp around the electrical issue with my girlfriends parents car is way over my head. The car is a 4x4 Octavia TDI 2009(or 2010) model.

Long story short: Took out a fuse due to a warning light that wouldn't turn off, put it back in and forgot to attach the fusebox cover properly. Car drove for two days in a rainstorm equal to driving under water and now the fan keep spinning when the ignition is turned off. Car empties battery of course and the car is now unusable.

Took the battery out to charge and decided to try to get the fusebox out to see if it could be fixed or replaced. I have a new box on hand for about 100GBP.

First question is how to get the darn fusebox out? There is so much plastic and rubber that I feel I'm working on a big lego car. Really afraid of breaking anything. I removed the small and big torx that where inside the fusebox but I'm not able to lift it. Any ideas?

Also, I'm hoping this is just a matter of getting it dried out, and maybe replaced, but I'm really afraid that there something else wrong due to the complex electrics in this car. Are there any failsafe to prevent the ecu getting damaged in situations like this? If everything else fails I was planning to charge the battery, drive it about 30 min to my local garage, but could this potentially be damaging to the car's ecu?