There's a technique that seems to work well for some of the bosses, particularly the end boss of Infection. The .hack//IMOQ games are sort of notorious it seems for instilling fear of their end bosses because they tend to be pretty hard unless you're overleveled for them. ^^
Anyways, the technique that I had great success with was to take two heavy hitters (actually, there are two in particular that I used, but I won't say explicitly who they are so I don't spoil anything, but if you'd like to know later on, send me a private message.

I tried most of the combinations, and there's one I found to be by far the most effective) and buy a ton of healing items and heal yourself. Because the healing spells aren't the world's fastest, and because your wavemaster won't last two seconds against the last boss, this strategy seems to be the most effective.
Also, I would recommend keeping everyone on your list not only equally leveled (which is a great point, Pursuer) but also equally stocked with good equipment as you never know who you might have to play with. Furthermore, it helps flesh out the story more.
Okay, I think I did that without any spoilers (other than "the last boss is hard" but what else is new?

)