I would not bet at all on the problem being with the batteries with 2 CEL codes pointing towards a Lean condition.

The codes indicate there is far too much air and the ECU cannot provide enough fuel to compensate. Most likely with the age/miles the large air hose between the MAF and plenum has a crack in it or another critical hose that connect to that large hose. Spray some brake cleaner around it to see if it momentarily plugs up and runs better at idle. If replacing it, use only OEM for a proper fit and it will last longer too. Best of Luck.

 

Get Dr Prius app or something equivalent, several available, and scope battery for cells state of charge.
Looks like you have 2 unrelated issues, one with traction battery and one with drivetrain. Reason you drive like a dream on FWY is because you drives pretty much like a regular ICE vehicle then.

 

I had seen information about the intake hose cracking, is there an aftermarket solution to that?

Are there other common things that can allow extra air? I saw some information about a evap purge valve sticking open as well causing too much air.

 

Not to sound sarcastic , but I saw a lot of information about many things. Then, one starts replacing and repairing based on guess and luck. Proper way is to get the issue diagnosed correctly OR guesswork repairs will cost more, than having it scoped professionally.

 

I believe I found the issue causing the lean condition. Knowing that the intake plumbing and purge valve are both common problems, I started investigating those.

Intake was fine, how the hose going from the purge valve to the evap line had gotten completely disconnected somehow. So instead of sucking in gasoline vapor when called upon, it would be sucking in fresh air as much as it could handle. So I believe that will correct that issue. I can't confirm that because it's not currently running.

I found a salvage yard with a battery nearby. It has a warranty so I should be able to return if there are problems with it.

If nothing else, between the two batteries I can surely make one good one.

Does anyone know if the individual cells can be replaced in these like they can on the Prius? Or do you have to replace the whole big block?

As a sidenote, information about common problems and failure points is pretty vital to fixing cars, for both the diy person and mechanics, so I'm not sure why the salty comments about information on a diy forum.

Because of information I found online, I was able to quickly find and fix a problem on my car this morning. Furthermore if you can get a problem narrowed down to a couple things that are common issues, you can usually replace parts diy far cheaper than paying a mechanic just to diagnose it. That's just my opinion.

 

Your highlander uses the same cells as the nimh prius and camry hybrids, the highlander just has more of them split into 3 banks rather than 1 large row like the prius. A skilled DIYer can replace individual cells, but you'd need to make sure they reasonably matched the existing cells.

Pine Hollow Auto Diagnostics recently put out a 4-part series where he diagnosed and replaced a couple bad cells on a camry hybrid. He's kind of shade-tree so it might be informative for DIY:

 

Thank you for the additional information. I hope it is able to help someone in the future. I ended up replacing the whole battery pack with one from a salvage yard. My goal was to sell the vehicle, and that got rid of all the warning lights and made it drivable again. My research showed the Highlander cells are different, they operate at a different voltage than that of the Prius. But I can't confirm that, it was just in various information I found. It seems the battery packs on the Highlander can have individual cells replaced as well, but it is more difficult because of the way they are constructed. You have to come up with a DIY solution to hold the cells together.