If I had fed a 0 IRE black signal to the screen then it would have been properly black as you suggested, in fact that is how we found out what was going on. I found an old signal generator that had a 0 IRE black and when we fed that to the screen, it worked beautifully. I thought that I'd cracked it and fed the borrowed generator into the video switcher for the next night's show. What I didn't realize was that the black as selected by the Technical Director running the show was actually internally made inside the switcher and that show was also compromised somewhat. Now I can laugh about it but at the time it was very embarrassing!
As Bill or someone else mentioned, it can be difficult to see the difference between the IRE levels. I'll add - depending on the ambient light. The gray noise that we got from our outdoor screen was invisible except at night so I couldn't troubleshoot it during the day.
What we eventually did until the manufacturer made an internal adjustment to the screen's control unit was to use a Time Base Corrector (TBC). You asked whether there was a device that could adjust the "setup" level etc. The TBC is an amazing device and can do almost anything "after the fact" as it were. Unfortunately I don't know of any that aren't rack mount and heavy. Perhaps someone else can jump in if they know better? However since you said that the projector is yours then you could make a test disc in Vegas, take that with you and set up your system as required wherever you are. You can use 7.5 IRE in Japan as long as you control all the equipment which it seems that you do???
As you said, the IRE setting for NTSC equipment to be used in the U.S. wherever manufactured SHOULD be 7.5 and that to be used in Japan SHOULD be 0 IRE.
Re: mastering, I need to check the latest mpeg encoder and I'll test some bars at work, then I'll get back to you. Sorry if I didn't answer all your questions but I'm a bit tight on time right now.