[Water Warrior 2]

First is kind of jumpy and clunky. Yup, they do that. Especially the first time when the engine and oil are cold. That is just the nature of many bikes. With time(as mentioned)parts will wear-in and smoothen out. Your bike and you you are relatively new so don't over think the situation. Use the manual to adjust the foot and hand controls to your own body size and shape. You need more saddle time to get the feel of the bike and after a while the odd clunk into first will be a reassuring sound.
To help reduce the clunk you can pull in and release the clutch a few times after the initial start of the day. This helps to free up the clutch plates from one another. It does work too. My Vstrom with 50,000km will rarely do more than a slight mild clunk and never lurch forward as it did when new.
Oh, before I forget and you probably don't know yet. The engine, transmission and clutch all use the same oil at the same time. The clutch is an oil bath design which makes it darn hard to overheat and damage.