Try leveling up some. I found that at the point I am at in .hack//Infection, that taking BlackRose and Mistral with me into a field 4 or 5 levels above my head and fighting the monsters in the field hanging on to dear life raised me 4 levels in less than an hour. All the sudden, the main quests became much easier. The data bugs are quite annoying, though. I've adopted the stratagy of avoiding them untill I can do my most powerful weapon attack (some sort of spinning thing marked as being level 2), then getting in close, performing the attack, and getting out, repeating untill the protect break finally happens.