I've added a category to a board but want to use a different timing method than the primary board, specifically IGT with MS. The only way of accomplishing this that I know of is to add it to all the categories which is what I don't want. How do?

Just manually remove MS from the categories you don't want to have MS in

You can't set different timing methods per category.

You have two choices here.

1. Manually edit each submission that fills out the wrong timing field, for all eternity (and believe me, there will be a lot). On the plus side, if edited well, your leaderboard will be more comprehensible to the casual viewer (they will know how your game is timed at a glance).

2. Don't use the speedrun.com "in game time" option, but tell runners to submit their in-game time to the "real time" field for this one category that uses in game time. That probably sounds confusing, here is an example: https://www.speedrun.com/hitmanbloodmoney The full game runs use Real Timing, but the individual levels use in game time (but it's not specified as "in game time" by the speedrun.com UI). This has the benefit of less moderation hassle, don't need to edit wrong submissions. It has the con of being more confusing to casual viewers and new players (need to read the rules more carefully before submitting runs).