I just ran into this precise problem. Thanks for the excellent explanation!

Thanks. Excuse my extreme ignorance, but by find the 95th percentile do you mean find the point above which the observations are in the top 5% of the distribution? This might be difficult since the range of values I'm dealing with can potentially be small, and the observed test statistic is higher than any observed value in the empirical distribution. Should I simply run more permutations?

Thanks for the answer. How should I go about recoding the data so that I can run the analysis?

Sorry I forgot to say. the check variable is the sum of the preceding columns and is there only to check if there is missing data across the other columns, as each one should add up to two.