I completed a perfect game for Xenosaga 3 and I utilized several guides on the web. Although most were close to having every item in the game and how to obtain it, none were completely accurate. I don't blame the authors because something of this caliber would take a completionist to discover all of these and most guides were probably written for players who just wanted to get through the game and side quests.
On this to note is that shops cycle inventory after every few episodes to allow for new items to come into stock. Because of this there are several items which need to be purchased before defeating a certain boss to move the storyline along. In some cases, namely the militia decent you will need to farm money in the stage before to allow you to purchase all of the equipment which would go out of phase during that mission.
I do not include the items which can only be obtained through hacking devices because I do not believe in such devices, preferring to play the game as it was intended. Items, which can be stolen or purchased, will be topped out at 99 each unless there is a predefined limit such as the carnelian eggs (max 3) and the Traps (max 10). You will not that the three skill keys are not included simply because these were used to max out the character's skill line. Equipment, that expired after a certain chapter was finished, was procured before moving on which involved a lot of grinding for enough money to purchase 99 units, before they became phased out. In some cases only a few of each item existed, indicating they could not be obtained through purchasing or repeatable stealing / drops.
You will note in some of the lists that I make mention of where an item is obtained and where other guides incorrectly omit it altogether. I hope this resource will help other players who are insane enough to undertake this challenge.