Choice Scarf is redundant with Diggersby's Quick Attack. Instead, use Wild Charge to let Diggersby hit Skarmory and other bulky Waters.
Substitute + Life Orb wears down Gengar fast. The only time to use that is when Gengar is using Pain Split, which is more effective the lower Gengar's HP is. Either use Black Sludge as the item, or use Pain Split over Sludge Bomb.
Actually, Mega Gyarados can get away with using Adamant, since its bulk is what makes setting up Dragon Dance easy: 24 HP/252 Atk/232 Spe Adamant still gives you more power while still outspeeding Noivern.
As an attacker, Zapdos is outclassed by both formes of Thundurus, as they're faster than it is and both have Superpower to hit special walls:
Incarnate Thundurus:
-Thunder Wave
-Thunderbolt
-Focus Blast/U-turn
-Hidden Power (Ice)/U-turn
Nature: Timid/Naive
EVs: 4 Def/252 SAtk/252 Spe
Item: Life Orb
Ability: Prankster
or
-Nasty Plot
-Thunderbolt
-Focus Blast
-Hidden Power (Ice)/Taunt
Nature: Timid
EVs: 4 Def/252 SAtk/252 Spe
Item: Life Orb/Leftovers
Ability: Prankster
or
-Thunderbolt
-U-turn
-Hidden Power (Ice)/Grass Knot
-Focus Blast/Grass Knot
Nature: Naive
EVs: 4 Atk/252 SAtk/252 Spe
Item: Life Orb/Expert Belt
Ability: Defiant
or
-Taunt
-Volt Switch/Thunderbolt
-Hidden Power (Ice)
-Thunder Wave/Focus Blast
Nature: Timid
EVs: 4 Def/252 SAtk/252 Spe
Item: Leftovers
Ability: Prankster
Therian Thundurus:
-Agility
-Thunderbolt
-Hidden Power (Ice)
-Grass Knot/Focus Blast
Nature: Modest
EVs 252 SAtk/4 SDef/252 Spe
Item: Life Orb
or
-Nasty Plot
-Agility
-Thunderbolt
-Hidden Power (Ice)
Nature: Modest
EVs: 128 HP/252 SAtk/128 Spe
Item: Life Orb
or
-Thunderbolt
-Volt Switch/U-turn
-Hidden Power (Ice)
-Grass Knot/Focus Blast
Nature: Timid
EVs: 4 Def/252 SAtk/252 Spe
Item: Choice Scarf
Edit: I think Excadrill may be a better fit due to it resisting Stealth Rock and not adding a Stealth Rock weakness to the team:
-Earthquake
-Rock Slide/Iron Head
-Rapid Spin
-Swords Dance/Substitute
Nature: Jolly
EVs: 4 HP/252 Atk/252 Spe
Item: Air Balloon/Chople Berry
Ability: Mold Breaker
Thanks for that in-depth reply. I've actually been experimenting with the Life Orb and Black Sludge variants of Gengar and I was feeling that he lacks punch without Life Orb, but then again it is nice to set up a sub, take something out and keep healing to a good level.
As for the Excadrill set, do you think Rock Slide/Iron Head is necessary for coverage? I was thinking of using Shadow Claw since it allows it to hit Trevenant and Gourgeist fairly hard.
Excadrill definitely helps solve the entry hazard problem, but do you think it's problematic to only have one special attacker in Gengar? I just feel like Will-o-wisp would case me some major headaches if I only have one special attacker.
Thanks a bunch for your help though and I'll definitely keep tweaking things until I get something that works
Waiting for Dunsparce Mega-Evo. FC is 3582 9525 5407