In the second sentence the coffee is consumed whereas in the first example not necessarily. In other words example two emphasizes the *completed* action, or the *result* of the completed action.

It's tricky and no matter what grammatically is correct, it's not uncommon to here people use the simple tense when they should use the perfect tense. In some cases, the meanings are the same such as with: "I'll wait here until you return." "I'll wait here until you have returned." But for me, with the intended meaning, I feel only your second sentence is right. I would understand the first to be the same, but I feel it technically means "have" as in "to possess" (before drinking it), whereas "have had" means to consume the coffee. ...I'm not 100% sure though.

Concatenation. "I have" and "I've" mean the same thing. The latter is used more in conversation as it sounds better. The "had" might indicate a completed action but the intent of both sentences is that the person wants a cup of coffee, likely to be awake. Both sentences are trying to say the same thing. Technically, the second sentence is better because the actions agree with a time frame: one can't work hard while having a coffee at the same time.