Lots of questions, if you can answer any that would be great.

Is that just when stopping? On our 2007 when it isn't fully warmed up sometimes when coming to a stop it sort of jumps around, like the motor can't quite decide whether it wants to be on or off. This only lasts a second or two. Once fully stopped though and the motor is off there are no more hiccups. It doesn't do that once it has warmed up. It has been like that for the full 6 (ish) years we have owned it. If a Prius feels like it wants to move with the foot on the brake after it has been stopped for a while then most likely the ICE is still going, which feels strange on this car since it is normally off in that situation. The ICE might still be going if the pack is failing, because the ECU doesn't want to shut off the ICE if it isn't confident it can turn it back on again.

 

As in, you took off all the pieces blocking the view of the ducting and it all seemed to be there?

I would suggest after warming the car up fully detaching the last piece, the one that pushes air out the side of the car over the 12V battery. Then turn it back on and verify that harm air is coming out where it should. An instant read food thermometer might be useful to measure the temperature of that air.

I'm trying to recall the details, but I believe there was a foam rubber baffle on the top of the battery whose purpose was to keep the cooling air near the modules instead of blowing out over the electronics section. If that was missing or damaged the battery might run hot.