If you want a good Manaphy set, use this :
Manaphy @ Wacan Berry
EV : 40 HP - 252 SpA - 216 Spe
Nature : Timid
- Tail Glow
- Ice Beam
- Grass Knot
No Rest, there is just no space for it. There is no point in surviving Scarf Zekrom Lightning Strike if you don't have Ice Beam to kill it, just like you need Grass Knot to OHKO Scarf Kyogre. Obviously, you need Surf so that you don't look ridiculous against Arceus, Jirachi and friends. Calm Mind Manaphy is better at Hydration-Rest anyway.
40 HP EV are needed so that Scarf Adamant Zekrom never OHKOs with Lightning Strike factoring Stealth Rock. 216 Speed + Timid to outrun base 95 like Rayquaza.
col49, your Rayquaza calculation looks wrong, there is no way Wacan Berry Manaphy can OHKO Rayquaza with Surf, I don't know, maybe you forgot that Air Lock negates the rain boost.
I feel like Ferrothorn should never be used without Leech Seed, it really needs it to make up for his lack of recovery, it also forces switches. The way I see it, you have two options :
1) Replace Spikes for Leech Seed and leave the rest of the team as it is
2) Replace Stealth Rock for Leech Seed and find another Stealth Rock user. Something like :
Specs Kyogre -> Scarf Kyogre
Scarf Palkia -> Support Dialga
Option 2) opens a DD Rayquaza weakness, so the choice is yours. But in general it's a not a good idea to rely on one Pokemon for setting 2 types of hazards, moreso when said Pokemon lacks reliable recovery. Dialga can also support your team with Roar, which can help your team against Substitute users that Giratina can't phaze