I brought out a LWB Shogun and box trailer about the size of your's last May. I will try to find the link/write up for you later.
Basically, if you stick to the toll roads, towing through Europe is no problem, though there is a sharp right hand slip road onto a precarious rusty bridge just outside Genova to worry about!
Your biggest problem is actually finding the right location for the ferry. Once there you join quite a queue to get on the Malta boat and it turns into a bit of a free for all. When you collect your boarding passes at the terminal building make sure you tell them you are towing a trailer to Malta and try to get towards the front of that queue.
If you get the same Grimaldi ferry we did, then vehicles towing trailers/boats were put on near the start. You have to drive in, up quite a steep boarding ramp, and turn around 180 on the car deck, so you are facing back out. (All loading/unloading is done via the stern)
Take your time and it should work out fine.