Body scanning feels a little stressful I feel a little stressed out when I move my attention through the body to observe the sensations. I am able to meditate far better if I focus on the entire body as a whole and feel sensations wherever they come up. 

Is this acceptable in the S. N. Goenka Vipassana technique or is it important that a mediator scan the body part by part?
I can't speak for the method taught by S. N. Goenka, I only know the part by part sweeping method (link to a detailed talk by Ayya Khema about the benefits of it), but I guess you do the same thing. As for this method it is quite usual to get stressed or tensed, because you have to be much more focused on the experience you may or may not find at the current spot you're keeping your attention on.
 Ayya Khema said it would be a very good sign if you get a feeling of nausea coming up when practicing it for the first time. In another context I heard a different teacher saying that it's like after cleaning your clothes your washbasin is full of dirt (because it was on your clothes). It may be similar with this technique since you have to notice all kinds of feelings or emotions.

She also mentioned that if you really don't like to practice this certain method, you'll benefit the most from doing it :)