Is there any source for the practice of not only dipping one's fingers into the Havdalah wine that was used to extinguish the fire and rubbing the eyes with it, but also spreading it around onto other parts of the body, and/or clothing, such as the forehead, the back of the neck, pockets, and any place with aches and pains?
Not sure about sources for most of these (although see Madeleine's comment to the related question).
But about the back of the neck, it may be related to the idea that this is the location of the luz bone (specifically, the protrusion where the knot of the head tefillin is placed - Arizal, Likkutei Torah to Judg. 4:5*); it is from this that the body will be reconstituted at the resurrection of the dead (Bereishis Rabbah 28:3). There are various opinions about what food (if any) the luz is nourished by; one is that it is from the havdalah wine (Maavar Yabok 2:6). So someone may have gotten the idea that some of that wine should be applied to the luz directly.
* Although several Rishonim (including Aruch and Rashi) identify it as the vertebra at the base of the spine.
I have a book with all the Libyan customs- Nahalat Avot and on pg. 74 it brings down this custom. However, some of the sources are unavailable. However, this book has a Haskama from: Rav Ovadia Yosef Shelita, Rav Mordechai Elyahu, Rav Eliyahu Bakshi Doron, and Rav Shelomo Amar.
Shulchan Aruch 296:1 brought by the Rema as a way to show that we cherish the mitzvah (this goes just for the eyes, I think that the others are built on the explanation of the Rema that we spill for to have a Bracha for the week to come so maybe people target those things needing a bracha.)