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.

 

There could still be a problem with the little swinging door mechanism where the warm air exits the inside of the car. If that was sticking in some way it could throttle the flow of cooling air even if everything else in the system was perfect. Probably not, but check it.

Our Accord had an issue vaguely like that where some of the little rubber boots that let water from the sunroof out into the wheel wells were jammed up with dirt and/or partially stuck shut. The water would then back up the tube and leak into the car instead. On the car it all looked proper but when the boots were pulled out it became clear why water was backing up. A similar issue affects the drain holes on the bottom of car doors - those get jammed up and then water rises inside the door and eventually drains out into the car rather than out onto the sill on the far side of the rubber door gasket and down onto the ground.