I'll propose two solutions here:
Because you're also running a Follow Me user, Physically Defensive Bulk Up Primal Groudon can work wonders on Mega Ray.
Groudon @ Red Orb
Ability: Drought -> Desolate Land
Adamant Nature (Naughty will work too, I know this is in-game, depends on what nature you got)
EVs: 252 HP / 252 Atk / 4 Def
-Rock Slide / Stone Edge
-Precipice Blades / Earthquake
-Steallth Rock / Dragon Tail / Rock Polish(kinda filler here)
Your Togekiss can Follow Me first turn, or Tailwind (if you're carrying it.) P-Groudon can just Bulk Up straightaway. It needs those boosts, cuz look at this:
+2 252 Atk Life Orb Mega Rayquaza Dragon Ascent vs. +1 252 HP / 4 Def Primal Groudon: 286-339 (70.7 - 83.9%) -- guaranteed 2HKO
In order to live Mega Ray's +2 Dragon Ascent, you need that +1. Two +1 Rock Slides take out both of those threats, or you can run Stone Edge if you want more straightforward destruction. Since you're using Mega Ray and Togekiss already, half your team's immune to Ground. So IMO there's not much of a reason to run P. Blades over EQ. The last one is up to you: Rocks will eat at Mega Ray the more it switches,
and if you're feeling risky then you can run both Rocks AND Dragon Tail. A +1 Dragon Tail smashes over 3/4 of its health, ensuring the SR KO next turn. Follow Me wrecks Dragon Tail though, so watch for that.
Oh, Klefki, you bloody rascal. Klefki is one of the MOST ANNOYING POKEMON EVER. So, of course, here's a set:
Klefki @ Leftovers
252 HP / 252 Def / 4 SpD
Typical Klefki fare. Unfortunately, this keyring doesn't get Taunt. ;-; But you can T-wave Mega Ray to scout for Lum Berry. We don't want to give them a free +2 Attack, do we?
Oh, but I forgot: Lord Klefki can take it.
+2 252 Atk Life Orb Mega Rayquaza Dragon Ascent vs. 252 HP / 252+ Def Klefki: 248-292 (77.9 - 91.8%) -- guaranteed 2HKO after Leftovers recovery
Yep. All around an annoying-as-heck crippler. Fun to use, not to be against.
--Caution: Iffy Sets Beyond This Point--
Golduck @ Choice Scarf
Ability: Cloud Nine
EVs: 4 HP / 252 SpA / 252 Spe
Cloud Nine is POWER. Scarf makes you outspeed Mega Ray, and if you suspect the Follow Me you can Icy Wind, and if not, you can Ice Beam. Or you can not lead with Golduck, and switch it in on a Ray that has used Dragon Ascent. You can then Scarfed Disable them.
Cresselia @ Choice Specs
EVs: 252 HP / 252 SpA / 4 Def
252+ Atk Life Orb Mega Rayquaza Dragon Ascent vs. 252 HP / 4 Def Cresselia: 305-360 (68.6 - 81%) -- guaranteed 2HKO
Cress TANKS that and gets off rather good damage with Icy Wind. It's got great synergy with P-Groudon, as it takes out the Strong Winds.