Mescaline is not red.
My theory would be, the more red the vinegar, the less pure the mescaline.
It should not take very long for mescaline to migrate from a non-polar solvent such as limonene into an aqueous acidic phase such as vinegar if the two are mixed adequately. All this talk of things taking days or even weeks is outdated and was most probably based on producing tinctures from plant material.
The aim of adding the vinegar to the limonene is to achieve a phase transfer by protonating the mescaline, which is dissolved in limonene as the freebase. Phase transfer time will be minimised (i.e. happens more quickly) by maximising contact between the two phases. This is achieved by thorough mixing.
Emulsions should not be too much of a problem with vinegar and limonene as long as you have taken care to ensure that the limonene is free from particulates such as lime particles or plant material.
If the limonene appears cloudy when drawn from the lime paste it can be filtered and/or left to settle for some time in a suitable container. It's generally easier to decant away from sediment if the container is relatively slender, although something like a boiling flask provides a shape that helps to trap sediment as well.
Once you have crystal-clear (albeit coloured) limonene you should be able to mix the vinegar through it quite vigorously and get the back-extraction done in minutes rather than days. Repeat the process with several small portions of vinegar. It does not matter if the vinegar is colourless - mescaline salts are colourless unless the anion itself is coloured.
“There is a way of manipulating matter and energy so as to produce what modern scientists call 'a field of force'. The field acts on the observer and puts him in a privileged position vis-à-vis the universe. From this position he has access to the realities which are ordinarily hidden from us by time and space, matter and energy. This is what we call the Great Work."
― Jacques Bergier, quoting Fulcanelli