not being an expert but having a keen interest... I was speaking with Dr. Thomas Blaha (Germany, Hannover Uni.), who has a book entitled Sustainable Animal Production. His Ph.D. student, Stefanie Rieper's thesis, Epidemiological studies on the use of veterinary diagnosis at the abattoir as animal-based animal protection criteria for assessing the Animal health and animal welfare of the animals in pig herds, at http://elib.tiho-hannover.de/dissertations/riepers_ws13.pdf (go to p. 134 for English summary). Counting lesions (lung, pleural, skin) at slaugther, recording these per herd. A six-month rolling average provide a benchmark for animal health and welfare assessemnt. Over time, vets can target the risky places for investigation and education and treatment. Can then link this data up to foodborne pathogens and use of antimicrobials, and foodborne illness rates...?
It's one of those things that's been looked at many times. Rob de Koning did a thesis that looked at this in real detail (R. de Koning. 1985. On the well-being of dry sows. PhD Diss. Univ. of Utrecht, Utrecht, the Netherlands.) and a lot of what is used subsequently has been a variation on his work, but in a much more condensed and workable form. My best advice would just be to look at the literature and you'll get a handle on the different ways people have scored lesions. The detail you can go into will depend on your available resources - that is "time" - and what your question is. If you want a handle on aggression-related lesions then your method may be different that one where you want an overall score taking other elements of the housing system into account - i.e. skin damage that might be related to pen fixtures & fittings.
You could use the Welfare Quality protocol for Pigs. It's basically developed for large numbers of sows because the end score is a 0, 1 or 2. But there is more detailed underlying protocol. See www.welfarequalitynetwork.net