Water Gem is kinda useless IMO. If you want a special Politoed, then have Choice Specs instead of the gem. Also get rid of Hypnosis and put Ice Beam. That way, you can do more damage to grass then HP Fire. HP Fire is useless in Rain, put HP Grass for opposiing Gastrodon't for 4x weakness.
But since Politoed is essential to this team, I suggest a defensive Politoed so you can last longer and come back in if another weather setter (Tyranitar, Ninetails, etc) comes in.
Politoed @ Leftovers / Trait: Drizzle / EVs: 252 HP , 252 Def , 4 SpD / Calm Nature (+SpD, -Def)
Toxic for more accuracy and stall. Hypnosis is for some damage done without interruption but it has some shaky accuracy. Scald is for powerful STAB and a ok chance to burn. Protect for some stall, or Perish Song to get rid Pokemon that set up, like Breloom or Toxicroak. Ice Beam for coverage.
Physical Gastrodon? Special would work better in this case. Stockpile instead of Curse would be good. It raises both SpA and Atk :D Scald and Earth Power instead or Waterfall and Earthquake. Then EVs: 252 HP / 4 SpA / 252 SpD Calm Nature.
Now half your team is water, not a very god idea. If you decide to go with Lapras though, Leftovers over Chesto berry. You can always switch into Politoed for rain.
I would suggest Latios:
Latios @ Choice Specs/Scarf / Trait: Levitate / EVs: 4 HP , 252 SpA , 252 Spe / Timid Nature (+Spe, -Atk)
Thunder for obvious reasons. Draco Meteor for powerful STAB, and Psyshock is also for STAB.
I think you are trying to fit defensive and physical/special all into one? Not the best choice. If you want a Desensive/staller, go with this:
Jirachi @ Leftovers / Trait: Serene Grace / EVs: 252 HP / 128 Def / 128 SpD / Trait: Bold (+Def, -SpA)
Wish for healing. Thunder Wave to cripple fast opponents. Stealth Rock to set up, if you want. Iron Head in the face of a taunt.
If you want a special Jirachi...
Jirachi @ Leftovers / Trait: Serene Grace / EVs: 128 Def / 252 SpA / 128 SpD / Modest Nature (+SpA, -Atk)
A couple of Calm Minds and you're good to go.
Black Sludge over Focus sash due to the common Spikes and Stealth Rocks. run Jolly. Swords Dance works well if you can stay in for a while without getting KO'd. Bulk Up for extra defense. Sucker Punch over Poison Jab and Drain Punch over Brick Break. You can also consider Substitute over Ice Punch, your choice.
4 HP / 252 Atk / 252 Spe
Masquerain is ok though I would definitely replace her. I suggest Breloom.
Breloom is pretty frail so watch out for that.
Breloom @ Toxic Orb / Trait: Poison Heal / EVs: 236 HP , 212 Atk , 60 Spe / Adamant Nature (+Atk, -SpA)
Spore is great 100% accuracy. Bulk Up is great +atk and +def. Drain Punch for healing and power with STAB. Seed Bomb is also STAB.
Hope my answer helped a bit :D