Alas, none to the above. The problem is that you're using passive mode when a more active construction is more natural.
The first is closest, and your impression is correct. Better would be, "After a vacation, you feel more motivated and ready to work."
The second is just wrong, although it has odd overtones which you probably aren't familiar with. There is a phrase "one more time, with feeling", which usually applies to playing music or acting, meaning "let's try it one more time, but this time (with enthusiasm / do it right). Since this phrase fits well with the latter part of the sentence, the effect is peculiar.
The third might be almost right, but obviously not what you intend. The construction "Do A while B" usually implies that you won't do A if not B. The phrase "while you are feeling" should modify "come". The result is that the sentence suggests that after a vacation you only come to work while you are feeling refreshed from the vacation (and that you may not come back after the feeling wears off).
If the writing previous to the desired sentence is also in the passive mode, or it focusses on the interior thoughts and motivations of "you", then the first choice is best. But if the subject of the writing is, for instance, a discussion of vacations, then the more active mode is preferable. An example might be, "Regular vacations increase productivity and improve morale. After a vacation you feel more motivated, etc."