Hey STEELDRAGON,
Solid team! I see the point is abusing Choice items to a great extent, which is not bad, only unnecessary with some pokemon. You obviously check most pokemon well except for Substitute users like Gengar and Zapdos, and Infernape.
I want to suggest using Gengar over Rotom-W b/c the mobility provided by Gengar is invaluable to your team. His set should look like Gengar @Life Orb | Timid Nature | 4 Def / 252 SpA / 252 Spe | Substitute / Pain Split / Shadow Ball / Focus Blast. I can see Gengar taking care of your Infernape problem. Substitute pokemon are simply hard to handle, but abusing them as setup fodder is their downfall. I suggest using the Dragon Dance set over the Choice Specs set; a good DD set is the following: Kingdra @Chesto Berry | Adamant Nature | 144 HP / 160 Atk / 40 SpD / 164 Spe. He doesn't get 2HKO'ed by Gengar or Zapdos, and can setup on many bulky waters which give your team trouble.
Now for the nitpicks, I would use a Modest Nature over a Timid Nature on Heatran b/c it gives you the power to OHKO Machamp leads. Although, a Modest Nature might take power away from Explosion, the Life Orb will make up for the Atk lost. You definitely want to use Ice Punch over Trick on Jirachi for Dragonite and Flygon.
Hope this helps and good luck!