I want to get into speedrunning Firewatch and I'm reasonably certain I can set a record for that game; but try as I might I can't get the load-time remover to work with my livesplits. Nothing I do gets it to work.

So my question is this. What is the best method for recalculating a run manually to remove load times? What program is the best for looking at the run frame by frame to be as accurate as possible?

I can't help with the manual recalculation. However I would recommend (if you haven't already) reaching out to the firewatch community to ask for help in setting up the load remover.