I have a 2015 Harley Road King and after 2000 miles, when I changed the oil in the chaincase it was grey and cloudy, which I assume is due to water in the oil. Now for the last two weeks it has been raining severely here in Hawaii and I ride my bike in the rain, even in very heavy rain. Is this what is causing the water in the chaincase oil?

I changed it because in first gear the clutch started releasing in a jerking way right at the end of the clutch travel and the dealer said that is a sign of moisture in the oil.

 

You shouldn`t have to change primary oil at 2,000 miles, even if you ride in a hurricane every day, water should not be able to get into the primary area.

What does the transmission lube look like, is it normal?

 

If oil's not leaking out of the primary from one of the seals or the gasket I can't see how water could get in. Unless it was there when you got the bike.
It's under warranty, I would get the dealer to check it out.

 

I don't think that you're riding the bike far enough or long enough to get it good and hot, up to operating temperature. That's causing condensation in the motors components. It'll take a good 30-45 minute ride or more depending on where your riding at to heat her up to the proper temperatures.

 

Today I changed oil and transmission and they looked ok. I'm taking it to the dealer to have it looked at when I take it for the saddle bags recall. I don't think it matters but I can be stuck in stop and go traffic for 40 minutes at a time using the clutch in the friction zone.