In general, you will want to upgrade your weapon whenever the magic attack and physical attack is increased. a +1 in damage is equal to a +10 in your primary stat. The same applies to armor. With accessories, there's a lot more leeway, but you usually focus on the primary stat when leveling. You worry about secondary stats at endgame when you're comparing items of the same ilevel.

Also, L53 dungeon gear (from Sohm Al), is i130. lv.54 gear will actually be marginally better than the augmented Magitek gear (You'd prolly replace armor and weapons, but leave accessories alone), and the lv.55 dungeon gear is just flat out better in every possible way. After that point, you should begin replacing all your gear when you get something of a higher level.