Next thing was to bring all the instruments together to the tempo mapped grid. I have made several modifications to Reaper to make editing life easier. First of all, I have a mode where when I click on an audio item, it creates a split at the cursor location. So I can put a split right before and right after a hit, with 2 clicks. I also modified Reaper so that if my cursor is at the top of the item, it moves the item, but if the cursor is at the bottom of the item, it slip edits the audio instead of moving the item. That makes it extremely easy to move a snare hit to the grid, for example. I cut the audio before and after a hit and slide it into place.
So, after accurately tempo mapping the song I then went though each instrument and slip edited the hits to match the grid. Remember I am not quantizing the audio, so the feel stays the same as how it was played, but it gets very much tighter as everything follows the drummer. While this takes time and can end up being a bit expensive, consider how much tighter my delivered mix/master is compared to the others where the timing was much looser.
I was during this editing process that I discovered the percussion tracks were misaligned. If I may go off on a bit of a rant here, I would like to say that this aspect was a true "separate the men from the boys" moment. Why would the percussionist continue playing in the stop sections, while then coming back in several bars late? It just didn't make sense, yet all the other mixes exhibited this issue. The only answer could be that the tracks weren't lined up. I moved the audio items so the percussion started with the other instruments, and wouldn't you know it - the stop times lined up too.
Assuming that all tracks line up and just going along with whatever happens regardless of the impact on the tune is an inexcusable rookie workflow.