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Ah, you have triple-element classes in front party. This may be why Djinn Storm is so devastating, because you spend extra turns at classes with lower multipliers. It may be easier if you switch to duo-element classes for the main group, since they will be slightly more durable while recovering djinn. Of course the downside will be that it will take longer to get to the 3rd stage.
Another advice I can give is to stack pp-recovery items on healers only, since you will be spending 50+ PP per round at least. If your attackers drop low, use Ether / Aroma / Ember.
Third advice is to replace Sol Blade with a Jupiter-unleashing weapon, since Doom Dragon is strong against Armageddon/Megiddo. For this boss fight, Sol Blade gains use if you use it as a stat-stick for "physical" Jupiter psynergy like Quick Strike and Death Leap.

I'm still kind of surprised at the damage numbers you report. Are you playing on Normal or Hard mode?

Also I suppose Gale instakilling bosses is probably unintentional, unless Caledor left it in there for speeding through the game for test purposes 

I managed to beat him with the party set up I had without using Gale. I just rearranged my front line to have only 2 tri classes and the other 2 were substituted with dual class characters. I definitely had to anticipate djinn storm in the third phase and make sure I had at least 2 tri classes in back line. I was doing near 800ish damage per unleash from the Dark Blade. It's a venus unleash and Doom Dragon is resistant to Venus lolwhat. Felix, who I has Dark Blade equipped, had his attack stat boosted to max and I just spammed Auto's and using Djinn like Lull to skip turns to get my Djinn back from Djinn Storm. Incredibly difficult fight for me, but I managed to prevail. I plan on doing Dullahan soon, but I am incredibly reluctant to attempt with my current levels.

Oh, Idk if this was an intended feature, but I used Gale at the start of Phase 2 of Doom Dragon and skipped the whole phase straight to Phase 3. Oh wow, I Gale can cause the final boss to be done in 6 turns or less. Gale will make the boss fly away and reduce his phase hp to 0 allowing the next phase. Was this intentional?

Indeed Doom Dragon has True Collide / Dark Contact, but it shouldn't be that powerful. It targets 3 members max, deals about 150-200 damage per character hit and sometimes heals for 50% of the damage dealt. At worst case Doom Dragon should take 300HP back by using it.

Regarding the difficulty with Djinn Storm + Cruel Ruin wiping you group, what is your general approach to the fight? How many attackers, healers, wild cards?

So, I misspoke. It does only hit 3 party members, didn't hit the fourth but he healed for like 650ish hp. He healed anywhere between 170hp to 290hp off each individual hit. I thought he hit all 4 the first time he used it on me and it caught me off guard, wasn't expecting the new attack! As for my set up I have this.

Lvl 44 Jonin 4 5 I'm using all the dark matter armor/wep on him with the angel ring. The procs from the dark sword are insane.
Lvl 44 Guardian 5 4 I have it where she has a decent amount of PP with PP recovery and some bonuses to Mars. Her gear is kind of all over the place.
Lvl 43 Pure Mage 4 5 Her gear is alright, I got a fair bit of mercury/jupiter power from items to buff my attack psynergies and I have a decent amount of PP/PP Recovery items.
Lvl 43 Destroyer 5 4 His gear is kind over the place too, but I find myself using him when I'm going on the offense or if I need to use some of his djinn. (I carry Flash and Coal on him)
Lvl 43 Chaos Lord 2 7 His gear is centered around Unleashes of the Sol Blade, Have Sol Ring, War Gloves, Hyper Boots, Mithril Shirt, Valkyrie Mail. I just spam auto attack and the occasional buff and/or djinn.
Lvl 42 Chaos Lord 7 2 Tbh, I just spam his Unleashes too with Excalibur and his gear isnt ideal. mostly tanky gear.
Lvl 43 Arcanist 7 2 Ivan has a fair bit of PP+/PP Recovery mixed in with +Ailment and some Jupiter Power increases. He's pretty solid.
Lvl 42 Arcanist 2 7 She has pretty much the same gear set up as Ivan. Pretty solid dmg/healer.

My general strategy for doom dragon has been to star the fight with Felix, Jenna, Piers and Ivan. I'll Shade with Ivan, use another mercury Djinn on Jenna, use kite on on Felix and I'll Haze Ivan with Piers (Ivan gets obliterated by this boss with this Djinn setup, as does Mia). I generally go for Eclipse summons and just try to keep party topped off while keeping damage up from at least 1-2 of my characters (Usually Isaac/Felix/Piers). I do well up until the third phase. I keep getting nuked by a djinn storm/chaos ruin combo. If I have people alive after the combo theyre too slow and get out sped by boss. It's essentially a wipe everytime he does that. I'm sure I'll think of something. I beat the 3 super bosses, not counting Dullahan, in the 40's. Star Magician was tough as hell.

Doom Dragon has proved to be a difficult fight for me. My average level in my party is 42. I keep getting him to the final phase then I get annihilated by a djinn storm plus chaos ruin. I also noticed he has some new moves, specially in phase 2 and 3. He has that AoE breath, not Darksol Gasp but I think a new ability, that drains HP from the whole party. Watched him heal like 1.2k in a turn from it ._.

I'm looking to farm some forgeable items, namely Orihalcon and some weapons from Inner Sanctum. I've been following the RNG guide but can never manage to get the drop. Anyone have any tips on how you farmed these items? 

I've never posted on here, but I wanted to make an account to reach out and just say I really appreciate this rom-patch. Golden Sun is one of my favorite games and as an adult having a version that balanced the game to make it more enjoyable to me. I beat GS TBS with this patch and I just beat Sentinel, Star Magician and Balgor. I have Doom Dragon and Dullahan left with a party of around lvl 40-41. It's been incredibly enjoyable to constantly mix djinn/classes up and I've thoroughly enjoyed this playthrough. Thanks!