Rain teams usually have problems being walled by Ferrothorn / Gastrodon & Jirachi, and this team is no exception. Most Rain teams are also vulnerable in getting swept by Virizion or Celebi, but you have Dragonite and Jirachi to mitigate this problem. Toxicroak, CM Jirachi, Sub DD Gyarados, and Tornadus are all big threats; Sub DD Gyarados and Tornadus are covered well by Jirachi, whereas Toxicroak and CM Jirachi are problematic to this team.
To solve your first problem of being walled by Gastrodon + Jirachi combo, I suggest NP Celebi over Ferrothorn. Jirachi and Ferrothorn provides redundant coverage to Rock and Dragon Types, whereas Celebi can take Grass, Electric, and Water hits like Ferrothorn.
Celebi @ Leftovers | Natural Cure
Timid | 240 HP / 64 SpA / 128 SpD / 76 Spe
Giga Drain | Earth Power | Baton Pass | Nasty Plot
Earth Power lets Celebi deal with Jirachi. SpA EVs lets it have a good chance at 3-shotting Scizor with EP+EP+ NP-boosted EP, as well as scoring a 3HKO on specially-defensive Ferrothorn with +4 Earth Power (which is easier to reach than you think). Baton Pass lets Celebi escape from Scizor or Ttar's Pursuit. The lack of Recover may stink, but Rain allowing leftover recovery, combined with Giga Drain and Jirachi's Wish usually sustains Celebi. Nasty Plot + Baton Pass to Starmie, Politoed, or Dragonite is a nice additional luxury.
As for Toxicroak, I suggest adding Jellicent over Rotom-W. It not only perfectly counters Toxicroak, but it also prevents CB Terrakion from spamming Close Combat and win. It is also a decent answer to Landorus and Mienshao. Jellicent & Celebi together provides better coverage to Fighting Types than what you initially had. Celebi, for instance, is faster than Lucario and OHKOs with Earth Power after a special-defense drop.
Jellicent @ Leftovers | Water Absorb
Bold | 252 HP / 252 Def / 4 SDef
Scald | Will-o-Wisp | Taunt | Recover
I also have a few suggestions on your Scarf Politoed: run Timid Nature with enough Spe EVs to reach 260 Spe. This way Politoed can also check Dragonite after a Dragon Dance. Hypno ScarfToed is good; I approve xP
I'd also consider Iron Head on Jirachi over Reflect. Iron Head in particular helps your team against Tyranitar, who can shrug off even Water moves after summoning sandstorm. As DetroitLolcat has mentioned, it is also a clutch move that helps Jirachi regain its health, allowing it to better accomplish its primary job of Wish-passing. Paraflinch is the only way Jirachi can beat CM Reuniclus, as well. I would consider it. Even without Reflect, Jirachi does not simply sit there, as you put it, since it has U-turn to maintain the offensive pressure of your team.
Hope this helps, dragone. Have fun!