Fine + deduction. It's not like they've cheated is it? Isn't it just a case of wrong paper-doing. Haven't really read about it, but guessing it's a similar case to in Brazil where Portuguesa was relegated because they fielded a player who had supposedly gotten a 2 game suspension over one.
I think overturning the results should be enough. If they've lost all 4 then it wouldn't have benefitted them anyways. Fine + results overturning would be more than enough, IMO at least.
Goal difference?
Well make all games 3-0 or something. These rules have to exist in the laws of the FA. In Brazil it's 3p + overturning of results. Portuguesa lost a total of 4 points and were relegated instead of Fluminense.