In sentence 1, both verbs, make and wake, are in the present tense, but in English the tense (i.e., the verb form) doesn't always refer to the obvious part of the timeline. Here you might reasonably expect the current time, but this usage talks about a rule that's true in general. You should have made your bed when you were a kid, you should be making it now, and you should make it for the foreseeable future. (At all times, after you're awake, of course.) This is sometimes called the enduring present tense.
In sentence 2, the normative aspect (the "ought to", the should) still expresses the general rule, but woke (the past tense of wake) conflicts with that rule since woke is confined to past action. This makes the sentence ungrammatical. If you want to keep the waking in the past, then you have to transpose the bedmaking to the past as well:
2a. You should have made your bed after you woke up.
Of course, that's not a general admonition; it's about just that time after you woke up.
So why does 3 work, with the waking in the present perfect (have woken)? The clue is in the name. The "perfect" means that the verb speaks about completed action, and the "present" means that the action takes places at any time up to the present or that it affects the present. That necessary reference to the present is missing in the simple past in sentence 2.
This is simply one of the uses of Present Simple:
"In exclamatory sentences beginning with here and there to express what is actually taking place in the present."
There she goes!
For other uses and as the source see here.
Best Answer
A present perfect is indeed better here, because ordinarily you would not be asking so much about the journey to France as about your visitor's present state: "Are you now in France for the first time?"
Although technically "coming" to France signifies the journey there, most Anglophone visitors would think of that action as "complete" only if they never intended going home again!
Similarly, we would not use it to refer to the current visit, but this.
Some other ways of expressing the same thing: