There's quite a bit of information about the shooting of "L'Uomo, La Bestia e La Virtù" in the book Orson Welles in Italia. I don't have it at hand, but a few things I remember reading:
Angelo Francesco Lavagnino did the music, and as a sort of in-joke, included some musical allusions to his Othello score when Welles' character appears on screen.
Sergio Leone and (according to imdb) Lucio Fulci worked as assistant directors.
This was apparently one of the jobs Welles took only to earn some money, and his contract stipulated that he be paid for each day of work, with no actual limit on the amount of days. He supposedly tried to draw out the shooting by causing little delays: messing up his make-up and beard, etc..., so as to earn as much as possible. I suppose it was a somewhat similar situation to the one he worked out for David and Goliath years later.
Finally, the producers informed him they wouldn't pay him anymore, so he stormed off the set. The rest of the scenes were reportedly modified to either eliminate his presence, or else filmed using long shots with a double. According to the Welles in Italia book, he left a farewell note complimenting the crew but cursing out the producers.
The book also mentions that at one point during production there was a hiatus, so Welles made a deal with the producers: instead of giving him his normal salary during those days, the producers would lend him the film crew to work on a project he was preparing. The scenes they shot were eventually used in the pier scene shoot-out in Mr. Arkadin.
I'm not sure if this is mentioned in Orson Welles in Italia, but supposedly Sergio Leone reported that the actor who had to run in front of the train (the peg-leg guy, I suppose), was afraid that Welles was going to get him killed by doing such stunts.