Being Japanese myself, I may not be the best one to give you suggestions, but anyway, here's what I can tell from my experience visiting places abroad and joined some "walking tours" there.
I think people visiting Japan want to experience Japan.
And it is difficult to say what manga all the people from different culture like, because each has different tastes and interests, there's no single manga that would satisfy everyone.
So instead of trying to show what
they like, how about showing what kind of manga
the Japanese like, for instance?
If your project is focused on Akihabara, maybe a brief explanation about the history of Akihabara (which used to be a place to go to get parts for radio, I heard) up to present day, and then show them what kind of things are special in Akihabara, maybe visiting some mega shops of camera/electronic products, a fewshops for anime/manga, figures, and one of the "maid kissa"?
There must be a lot of visitors who love anime/manga and want to know what is "the latest" in Japan and also other visitors who are not particularly interested in those things but still want to see what kind of place Akihabara is.
The projects sounds great, I hope the tour or you're going to organize will be a great success!