Hey, so I have some comments on this analysis.
I think there is a fundamental misunderstanding as to what a lure actually is... The purpose of Wacan Berry isn't to "lure in" Thundurus, but rather, to survive its Electric attacks (among others) with relative health so that Manaphy can continue its onslaught on the opposing team. In other words, Wacan Berry isn't a "lure", it's simply an aid the keeps manaphy from being taken out too early so that it may keep sweeping. Implying that it's a lure is saying that you want Thundurus to come in on you, which you really should avoid if possible.
This is in the usage tips, but should probably be in the teammates section. Although, I probably wouldn't state that line anyway. Manaphy is a wallbreaker itself, so it appreciates Pokemon that can clean up after it as opposed to additional wallbreakers. Think Deo-S, Talonflame, etc.
Chansey is the better Pokemon to mention here for obvious reasons. Even so, neither blissey no chansey will try their luck staying in on these Pokemon, so this is where the whole "lure" factor comes in. Basically, stuff like Knock Off Thundurus and Knock Off Landorus would be better as they can actually draw in Chansey and seriously cripple it.
For the checks and counters section, you're usually supposed to list the best counters at the very top. In other words, why is Clefable second to last on that list? It should be first because it always beats Manaphy one-versus-one, whereas everything else on the list can lose if Manaphy carries a specific item, or adjusts its moveset.
Wacan Manaphy can actually beat this thing. I'd mention assault vest Raikou in its place because it can actually tank a +3 Surf even after rock and deal with manaphy relatively easily. In regards to offensive checks, AV Raikou is the best one bar none. See this calc:
+3 252 SpA Manaphy Surf vs. 0 HP / 0 SpD Assault Vest Raikou: 204-241 (63.5 - 75%) -- guaranteed 2HKO after Stealth Rock
This is fairly impressive and it's kinda disappointing not seeing Raikou anywhere on the list while Pokemon like Mega Manectric of all things are... =/
As for the main set, I'm kinda questioning the use of LO considering the whole appeal towards using Manaphy as a sweeper is that it hits hard af after a boost and is relatively bulky, making it difficult to take out, Life Orb just kinda diminishes that altogether. But I suppose that's better left for QC to discuss, though do take this idea under consideration at least.
As for the Calm Mind + Rain Dance set, that seems like something that's better equipped for Suicune, or rather it's outclassed by Suicune, but again, this change is rather controversial.
Other than that, this analysis looks pretty solid.