Hey,
So you've ended up with a pretty solid team after all the changes that have been made. First off, simply max hp and sp def on Gastrodon and change the nature to Calm. There is no use whatsoever in those def evs, Gastrodon needs the special defense for big threats to your team such as NP Thundurus or Tornadus. Replace HP Electric with either Ice Beam to hit Dragons or Earth Power for another STAB attack. Your team already handles Gyarados excellenty, in Rotom-W and Politoed you have two great checks to it.
I'd also like you to try out Perish Song on Politoed over one of you water moves. Perish Song is an excellent move to annoy ShellSmash and is a great way to defeat bulky stat-uppers such as CM Reuniclus or CM Latias late-game.
As is stated above, if the 52 Sp Def evs on Rotom aren't doing anything for you then change the spread to 112 HP | 252 SpA | 144 Spe which allows you to outspeed all Tyranitar and Adamant Breloom.
This isn't necessary, but you can also try out an offensive Deoxys over your current one. Offensive Deoxys still defeats Ferrothorn and Skarmory as you wish, but now poses a much more offensive threat. Expert Belt is the preferred item as Deoxys is mainly concentrating on coverage. 40 Attack EVs is enough to OHKO most Tyranitar, while the rest can be used to maximise special attack and the remaining put into speed with a Naive nature. The moveset is Superpower | HP Fire | Spikes | Psycho Boost. Psycho Boost is mainly filler, but it provides an extremely powerful STAB attack, which does a lot to neutral targets. Other options for that slot are Ice Beam, which retains the coverage you had with Ice Punch, or Shadow Ball to hit Reuniclus.
Great team, and good luck!