So, this started after swapping the deteriorating factory intake for a short ram cold air setup. Occurs more often in cold weather but it's hit or miss and much less likely to happen than not happen. It's pretty loud and has been doing it for years without a consequence. I've searched around before and saw others online with the same complaint but the Honda forums couldn't muster up the collective brain power to even understand what the people are talking about.
It's definitely not motor or trans mounts.
I believe it's the throttle body slapping shut real fast during whatever transmission protection Honda has built into the tune. It's seems to briefly suspend power during the shift to reduce wear and tear. It is absolutely related to the short cold air intake being on the car.
Only once has it done it on the 2/3 shift and that happened going downhill. Downhill acceleration seems to increase it happening.
My friend and I have talked about putting a micro camera into the intake to see if we can figure it out. This car is in great condition and has been in the family since it was just a few years old.