Don't align anything according to their initial transient. You're close mics can not be perfectly in phase with each other because they're spaced all over the damn kit. LEAVE THEM ALONE. Flip the polarity on your overheads to determine the best sound. If needed, you can nudge them A TINY BIT to get them a little more in phase, but if you just align the initial transient then you're killing the space and depth you get from overheads. You could move the rooms around a tiny bit as well if flipping the polarity doesn't seem to help.
All this SHOULD be done before you ever get keeper takes. Always flip the polarity of your overheads and rooms to get the fattest sound, if that doesn't seem to do anything, try moving them a little and go with what sounds best. I've honestly never seen a pro engineer have to move a ton of drum tracks around to phase them. They're supposed to be all far apart because they're at different distances.