GameFAQs provides a Perfect Game FAQ that covers rare and missable items, materia, and the like in detail. While the guide is not perfect--the last time I checked, it didn't note that one can keep the A, B, and C Coupon rare items--it's very close.

"Ultimate files" can take on a number of definitions. Do you intend, for example, to get at least one of every item, or the maximum number of every item? I've been working on the latter on and off for a long time, and I can assure you that patience, above all else, is critical.