Back in Contigo, ignore everything for the mean time and head to the house at the north. Inside, Issac, Garet, Ivan and Mia will be waiting for you. After the discussion about why Felix is doing what he's doing, Hamma will show up and inform you that you've unbalanced the elements.
You now have your old GS party back, and if you updated your save, they'll own everything they did before, otherwise they will start at Level 28, with basic equipment, and an incomplete Djinn collection. Djinn are the most important, because without all 28 from the first game you can't go into Anemos Inner Sanctum to get either Charon or Iris. You might want to take this chance to equip everyone with whatever they need and switch equipment around.
Unfortunately the only services available are the Sanctum, Inn and the minigames, since everyone's at Atteka Inlet putting the finishing touches on your boat. You can, however, get a Mars Djinni you were previously unable to. Go to the stump at the top-left of the main town area, and use Force (providing you got the Orb of Force transferred from the original game) on the stump to evict Shine, who will join your party without a fight.
Once you're done with sorting out your new additions, go back to Atteka Inlet.
Atteka Inlet Revisited
First of all, head down to the boulder in the enclosure at the bottom. Use Lift (providing you have the Lifting Gem) to lift the boulder up, then use Cyclone on the weeds inside to unearth Geode, the Venus Djinni! It'll join you without a fight.
Once you've got it, head back to your boat. Climb up and Hamma will be there to greet you. When you try to get on, a man will rush and drop off a chest. It is imperative you get this - it contains some Orihalcon, the best and rarest forgeable material in the game.
When you're ready, go ahead and set sail. The reef to the southwest, when on the world map, can now be hovered over using the B button. You can fly faster than normal when hovering, and reefs won't hinder you anymore (the rocky spires will, but the flat reefs won't). Another bonus of flying is that you won't get any random encounters. The downside is the meter above your boat - this is everyone Psynergy level. If you notice your party status at any point, and you've been using the flying mode a lot, you will realise everyone's PP will have dropped dramatically. So basically, use this in moderation.
You can now get a combo summon, Coatlicue. Go around Atteka to the split beach on the eastern coast. Fly your boat along the coast southwards until you get to a short river coming down from a mountain. Fly over this, then go left in between the trees around to another short river coming from a mountain. Drop your boat either in the river or on the southeastern side, then get off and enter Atteka Cavern. Inside, go around to the right so you can reach the water with Parch. Use it to drain the pool, then go back around, climbing up and down ladders to reach the tablet. You can now summon Coatlicue! She requires 3 Jupiter and 3 Mercury. She does no damage however - her effect is a weak initial heal, followed by 3-4 turns of awesome health regeneration - basically, your characters regenerate just over half their maximum health every turn for 3 or 4 turns.
Get back on your boat and fly back to the sea. Now, you will want to head back to Yallam.
Back to Yallam, Again
You've acquired some forgeable materials you will want to forge - a Dragon Skin, some Dark Matter, and some Orihalcon. You can get what you want from the Dark Matter and Dragon Skin, but you can reload over and over with forging the Orihalcon to get Excalibur. Excalibur is one of the strongest swords in the game, not that far behind the Sol Blade. Its unleash is amazing, capable of doing at least 300 damage, sometimes even 800. So, fly down between Osenia and Tundaria. You can now use your flying ship to save time and fly over land around the rocky spires separating the two seas, and get back into the Eastern Sea. Head north to Yallam and forge your stuff.
However, you will be able to get some more Orihalcon soon, so it doesn't matter if you don't get Excalibur. There are a lot of other great items to get from it, like the Xylion Armour. Whilst you're here, you can also get another great weapon. Use Force (if you have it) on the log outside the blacksmiths to form a platform you can hop to. Over on the other side, use Cyclone to uncover a ladder. Go down through the cave and grab the Masamune from the chest. This is excellent on Piers.
SW Atteka Islet
Now, sail back to the Western Sea, to the island hanging precariously close to Gaia Falls on the western edge of the world. It's southwest of Atteka; hence, SW Atteka Islet. Sail there, get off on the beach and enter the area. Climb down the vines and shove the pillar off into the water. Go back up and shove the box out of the left hole in the fence so that it drifts off the watefall and gets caught by the pillar. If you didn't update your save, or you missed any number of Jupiter Djinn in the first Golden Sun, a random one will be here. To reach it, use Lift on the boulder at the top of the area and jump across the pillars. It'll join your party without a fight. Anyway, go back down the vines and jump across the caught box to reach the Dragon Skin in the chest. Hold onto this for the mean time - there's no point in going back to Yallam yet. Leave the area and get back on your ship. You've got some loose ends to tie up at Shaman Village, so head back up to Hesperia.
Shaman Village Cave Revisited
If you updated your save with a GS game where you had won Colosso, then you'll be confronted by three of the gladiators that took part, that Issac beat. They'll say that Psynergy was cheating, and that they've come to get revenge for losing. They're remarkably easy to beat - if you want you can standby Djinn before the battle and summon rush them all on the first turn. They have about 600 health apiece - Eclipse and Meteor can take them down before you've even got halfway through your turn. When you win, you can pick up the Golden Shirt that they leave behind. This slips on underneath a character's armour, so equip it to whoever you feel needs it.
Once you've got it, head up through the top door. Lift the right-most boulder, then go around to the left and Lift the one on the other side of the Mercury Djinni on the rock above. Now, head back to the left-most boulder and Lift it. Go up to the puddle and use Frost on it. Go up to the ivy at the top, and blow it away. Climb up, and jump across the ice pillar, then across where the unlifted boulder is. The Mercury Djinni will attempt to run away, so follow it. The Lifted boulders will trap it, so save, standby Djinn and confront it. After obliterating it with summons, Eddy will join your party. Now, jump back across to the left-hand side of the room, and go back across the top. Head out of the cave this way and head back into Shaman Village.
Back here, use the Inn if you need to, and head back to Trial Road. You have to go back through all the puzzles, but you aren't pushed for time and you don't need to relinquish any of your items to open doors. You can grab all the Vials and Potions from the chests should you need them. Once you're at the summit, you can use the Hover pad to float to the platform and enter the cave. Lift the boulder inside (this is why you didn't come back earlier). Head down the long set of stairs to the open air section at the bottom.
Cyclone the bottom left weed here to uncover a Mad Plant. Beat it to earn yourself a Lucky Pepper. None of the other weeds hide anything. You may notice the Reveal symbol around the pools - the bubbles are actually platforms. Use Reveal to jump across the top platform and get an Elixir from the chest if you need it. The Jupiter Djinni at the bottom will constantly stay on the other side of the pool from you, so walk around until it's either directly above or directly below. Use Reveal and hop across. The Djinni will become confused and leap away, dazed. Approach and defeat Gasp in battle and it will join you.
Go back up through the cave and slide off the groove, then move the pillar into its slot and climb up. Go back through Trial Road (you can go back down the other route and get the other items if you want), and when you get back to Shaman Village, use whatever you need to and leave for your boat, going back through Shaman Village Cave.
Now, back on your boat, leave Hesperia. Look for a small beach split by a river on the western coast of Gondowan (southwest of Kimbombo, or southeast of Contigo). Sail up the river until you get to the thick river leading down the middle of Gondowan. Sail north until you get to a rock in the river that you can't get past, and disembark on the west bank. Go north over the bridge but ignore the familiar-looking red rock up ahead - go northwest and follow the path to Gondowan Settlement.
In here, one of the middle gravestones to the right has a Lucky Medal. Now, use Cyclone on the weed to the left of the fence in the left of the settlement. Down the stairs you can get a Star Dust from the chest. Now, do any necessary healing (there isn't an Inn or a Sanctum, so use Revive, Psy Crystals and Healing Aura instead. When you're patched up, go back to the red rock.