1. Warmest water, but not whale shark season. If you want whalesharks, then I suggest August or September.
2. Deep Blue, Peter Hughes Sky Dancer, or Galapagos Aggressor I or II. That's the order I would choose now.
3. Yes, but you need to let them know ahead of time.
4. If you mean land trip in the Galapagos, I'm not much help. Deep Blue doens't do land excursions. PP and Aggressor need to confirm if they still do land. Aggressor has a permit I believe.
As for other land tours, I recommend starting from Quito as as opposed to Guayaquil. We have toured Quito and done side trips to 1) Cloud forest at Bellavista 2) North to Otavalo and surrounding areas, staying at a Hacienda and 3) Visited Cotapaxi volcano. All were good, but Otavalu stood out as the best experience.