I am stumped

Hello All. My 2005 Prius has me baffled. I don't even know what to put in the thread title. The car has 209,500 on it. I'm an aircraft mechanic by trade and have more than kept up on the maintenance for this car. At 150,000 miles all cooling pumps, belts, hoses, spark plugs, all fluids, etc were changed. The hybrid battery was also changed about that time due to a few cells starting to show weak charges. I replaced it with an OEM Toyota Panasonic from the dealer. The car has ran great until recently when it started doing a variety of strange things. When it acts up, it seems like it has a hard time figuring out if it should be charging or pulling from the traction battery. The monitor will show as low as one bar and the arrow between the motor and the battery will flip flop back and forth as if it can't decide what it needs to do. Acceleration is poor as you would expect and the transmission feels like it is actually shifting gears when accelerating. It will start out normal from a dead stop and then almost immediately feel like it kicks down trying to accelerate. With your foot is into the pedal the car will eventually reach what ever speed your'e attempting to maintain. Decelerating may or may not charge the traction battery according to the monitor. When the car is acting up the AC blows warmer than normal and the power steering feels weak and requires more muscle to turn the wheel. The headlights also flicker bright and dim like you would see on a police car (regular halogen).

Using my Techstream I have thoroughly gone through every system and module without finding the slightest hint that something is wrong. Absolutely no codes, sub codes or any errors on the Techstream, dash, or display. Ever. The traction battery is strong and the highest difference between cell charges is about .03V, the 12V battery is brand new (replaced but probably didn't need to). The starting battery maintains about 12.5V overnight and shows 14.3ish when in ready mode. I have checked grounds, plugs, harnesses-pretty much everything I can think of. The inverter pump is running strong. This mostly seems to happen when it is hotter out (I live in the desert) however it's never consistent. Rain and moisture don't seem to make a difference one way or another. Extreme heat 110F+ is about the only time that I might be willing to bet that it may act up and even then it's a crapshoot. Overall it's been acting up less often but still will act up out of the blue. Shutting the car off and turning it back on does not fix the problem.

On two occasions over two back to back days the engine ran rough like it was misfiring and shook violently with a loud clatter but only for a brief moment. Once it happened immediately after starting and once while driving down the road. Both times by the time I got the hood opened it was running smoothly again. That particular issue hasn't happened for several months now. The engine purrs right along. Burns no oil between changes at 5,000 miles.

This is throwing for a loop and I'd love to hear your thoughts. If I had to guess I'd say it has something to do with the inverter but being intermittent and throwing no codes I'm hesitant to tear into anything yet. The ONLY thing that I've possibly come up with is that the fins on I the lower part of the condenser have been mashed pretty good from rocks and debris going through the grill and I'm thinking that possibly the lower part of the radiator behind the condenser (which is for the Inverter/Transmission if I understand correctly) is not getting as much airflow as it could. Both fans are running low or high as necessary.