Do the Ruins, the Sunken Desert, the Sun Stone, the Rainbow Shell at Giant's Claw, the Trial (which comes out of the rainbow shell stuff), and then the Geno Dome.
You could conceivably do the rainbow shell and trial quests first to get the Prism items from Melchoir, but all of the sidequests before the Black Omen should be manageable with the armor you already have.
Addendum: If you use Robo as a primary party member, it will be worth doing the Geno Dome first to get his awesome Crisis Arm weapon. Just make sure the last digit of his HP is 9 (which you can ensure by equipping the Gold Earring to max him out at 999) and he'll do devastating damage.
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