2017 prius rough idle and TONS of codes, help!

2017 prius two, 240k miles. getting numerous codes that just keep coming back. it runs fine when cold. then once warmed up it will not idle properly and keeps throwing all these codes. I've completely replaced the head gasket. new thermostat. new maf sensor. new ect sensor. rerouted coolant lines because heat exchanger was leaking. hybrid battery appears to be fine. spark plugs are working. I've cleaned the throttle body. it runs if I keep on the gas but shakes like crazy if I let off. I don't understand how all these codes keep getting thrown. I actually just went ahead and took it out and drove it up and down the road and it seemed to have no problem once I got it above idle speed I can drive all the way up and down the highway with no check engine light or anything and it did just fine. It's only when it slows down to around idle speed that it starts jerking and running rough. After I drove it about 10 miles I brought it back to the garage and as I was pulling into the garage it started jerking again and then threw up the yellow triangle and the screen says "check engine" and the check engine light came back on as well of course. please help.

 

Those are current. I am going in and clearing all of the codes and then the next time I try to run the car all of those codes come back again

 

Oh by the way, no I did not take it to a machine shop, however I know the engine has not overheated since I fixed the head gasket. I have been watching the engine temperature anytime I have started the car. The car has never even ran for very long because of this shaking issue at idle. I did take it for one long drive for about 5 MI to see what would happen but I watched the temperature of the entire time and it stayed at 190 the whole time. Well there was one time I was testing it before I found out that the heat exchanger was leaking coolant and the engine temperature did get up to around 210 and I shut it down at that point.

 

So I just went and bought a new 12 volt AGM battery because the one that was in there from the previous owner was a standard battery not an agm. I did a 5 volt reference test to my sensors such as the ECT sensor and I was only getting 2.5 volts when I should be getting 5V. After replacing the battery now all the sensors are showing 5 volts like they should. I was feeling optimistic this was going to solve my problem but after clearing all the codes and starting up the car again it still was shaking like crazy until I push on the gas pedal to rev up the engine and then it Smooths out but as soon as it gets back down to idle speed it just wants to shake. I went ahead and took it for a drive anyway and every time the engine would get to the point where it would want to shut itself down it would start shaking and just like it did to me two days ago once I got back from my drive and went to pull up to my garage suddenly the screen popped up "check engine please pull over to safety within the next 3 Mi and shut down your engine" and the check engine light came on. I pulled into the garage and ran the codes once again and this is what I am getting. There is only one active code for engine failing to start. It is running however it just refuses to run smooth in idle

 

yep. I cleaned the throttle body first. didn't work. so then i replaced the whole throttle body, still no. i did unhook the 12v battery to reset everything. got a new agm 12v battery. still no. it has a new air filter. I've changed the spark plugs. I've checked both ect sensors and wires. maf sensor i switched back to the original. fuel pressure checked and running well at 50. no pressure loss at 15 minutes so no leak from fuel injectors. the ignition coils have to be working because it runs and drives at faster then idle speeds. so frustrated right now...

 

I reset everything by unplugging the 12v battery and I cleared all codes, but i did not put it in maintenance mode.

 

I understand, but I have also worked on several Priuses and I have taken off the throttle body and cleaned them numerous times and never did this procedure and they all started right back up and ran just fine. So I have a hard time believing that's my problem but I'll give it a shot and see.

 

I believe I finally figured out what's wrong. I replaced the head gasket on this engine and I happened to have an extra gen 3 engine sitting around and when I was putting this one back together I felt like the fuel injectors didn't look that great and the ones I had in this extra Generation 3 engine looked good and from what I could tell looking at them they appeared identical so I put those in this engine because I felt they looked better. I just now got to thinking about that and looked it up and they are indeed different. So that makes total sense why it's not running quite right and acting like it's running lean because the fuel injectors are different and they are not spraying the proper amount of fuel. This has to be my problem. I'm going to switch them out today or tomorrow probably and hopefully this will solve the problem!