2005 Prius w/ "rod knock" - Looking for 2nd opinion

Hi everyone. Long time reader, first time poster.

My 2005 Prius has been running real rough for the past couple months. I was stubborn and tried to diagnose and fix it myself, but after 2 months of doing that and continuing to drive with the problem, I finally caved and brought it to a mechanic. They tell me it's "rod knock" and their estimate to fix it is $10,000 USD. They also said that engine is about to blow and I shouldn't even drive it home. Even if they're overcharging me, with 215,000 miles, sinking money into an engine issue probably isn't worth it. As you can imagine, I would like to exhaust every other possibility first.

Symptoms:
- It immediately started running rough after fueling up at an Exxon. I'd driven 800 miles in two days, but otherwise that there were no warning signs I could tell leading up to it.
- The CEL came on right away. Faults were 0P0300, 0P0301, and I think 0P0303. The other two cylinders were pending.
- When I drive, the CEL flashes on and off spastic-ly(?)...for lack of a better word
- It has more or less steadily gotten worse the more I've driven it
- At this point, when idling, it sounds pretty similar to this video:

- As soon as I put it into drive, the clanking noise goes away, but you can still really feel it running rough through the steering wheel and the seat (like sometimes I'll hit the wrong button on the radio because of the shaking)
- At certain speeds it feels like it goes away
- Accelerating sometimes makes it worse (especially at higher speed it's like it's kicking back), but it seems like other times when I accelerate there's no change. When it does kick back like that at high speeds, the Traction Control Warning light will sometimes come on for a sec.
- As I slowdown to a stop the shaking gets very noticeable again
- Last oil change was about 10k miles ago (was going to do it this week)

Fixes I've Tried:
- Checked for any obvious loose wires or hoses
- Put in all new spark plugs. Spark plug #1 (closest to pass side tire) was very rusted when I took it out. This is possibly (probably?) due to a missing fender liner on that side allowing water to kick up under the hood on that side. The coil next to it had a little condensation too but no rust. I dried them out and cleaned everything the best I could. Faults remained the same.
- Rotated the ignition packs and the faults remained the same. Tried the thing where you disconnect them one at a time, but the engine would just die and I'd get the red triangle.
- Cleaned MAF sensor and throttle body
- Checked resistance on fuel injectors
- Checked 12v battery is at correct voltage (heard this could cause weird issues)
- Only using "Top Tier" gas brands since the problem started
- I used Techron gas additive once and it seemed to help but only temporarily

Other things I plan to check before giving up all hope and buying a bicycle:
- Clean out / replace fuel injectors (unclear if I can just pull the fuse for the fuel line or if I have to take out the back seat to disconnect the power... Anyone know?)
- Check for air leaks (Not sure the best way to do this? DIY method?)
- Replace PCV valve
- Replace fender liner

If anyone has any other insights or suggestions, I would REALLY appreciate it!

 

I'd be thrilled if cleaning the injectors solves it! First thing on my list is to try a DIY fix like this:

The quote is for installing a new engine, plus "other things". They said they'd email me a full breakdown of the diagnosis and estimate which I'll post when I get it.

The thing is, they were being a bit vague about if the mechanic test drove it or not and how fast went (he was conveniently out for lunch). I took it on the highway when I drove home, and the noise and shaking goes away when I'm accelerating at higher speeds. From what I read, the rod knocking should speed up as the engine speeds up, correct? Or maybe I'm not understanding something about how hybrid engines work?

It's called "CAN OBD2 Memoscan U480". One of the things I'm waiting to get back from the mechanic is a list of the more detailed faults...

I was regularly (and it was normal) but I've slacked off a bit recently. Will check it again today.

I'm struggling to find the right way to describe the CEL. It seems to flash at the same rate as the car shakes I guess? (For example: At idle and low speeds it's solidly on. Then as I speed up it'll shudder on and off rapidly with the shaking, then stay on for a bit, off for a bit, then shuddering again.)

I also forgot to include in my original post that after this happened the MPG tanked to around 18-20 MPG.

 

Yikes. Good to know. I read on these forums that 5k is the official recommendation, but 10k for a Prius is fine. Guess you shouldn't trust everything you read.

This is the first time I'm changing the oil since I got the car...not sure how often it was changed before that, but it seemed the previous owner kept it pretty well maintained, so I'd assuming frequently.

The issue started around only 6 or 7k after the last oil change (only one I have a record of), but it definitely could be related...

 

Interesting thought. I read up on water in gas, and I don't think it's quite it (no stalling, starts up fine, no white smoke...)

 

Okay so the loud, sputtering clanking sound (like in the videos me and alftoy posted) ONLY happens in Park. I searched the forum a bit and didn't find anything.

As soon as I put the car in drive, reverse or neutral, it goes away.

The while I'm driving shaking is still present, but again, it doesn't always happen or speed up when I accelerate.

Is this be consistent with rod knock?

 

Thanks everyone for responding so far. It's much appreciated.

Based on the way the mechanic has been jerking me around, I have a hard time believing anything they've said at this point.
Getting a copy of the fault codes from them was like pulling teeth, but here it is:

(They used an Autel MaxiSys if that's helpful...)

Current:
P0300 - Random/multiple cylinder misfire detected
P0301 - Cylinder 1 misfire detected
P0303 - Cylinder 3 misfire detected
P0304 - Cylinder 4 misfire detected
P0171 - System too lean (bank 1)
C2318 - Low voltage error (power supply fault)
C1241 - Low battery positive voltage or abnormally high battery positive voltage
B1421 - Passenger solar sensor circuit

Pending:
P0300 - Random/multiple cylinder misfire detected
P0301 - Cylinder 1 misfire detected
P0303 - Cylinder 3 misfire detected
P0304 - Cylinder 4 misfire detected
P0171 - System too lean (bank 1)

History:
P0300 - Random/multiple cylinder misfire detected
P0301 - Cylinder 1 misfire detected
P0303 - Cylinder 3 misfire detected
P0304 - Cylinder 4 misfire detected
P0171 - System too lean (bank 1)
B1411 - Room temperature sensor circuit
B1271 - Combination meter ECU communication stop

----
I haven't taken the time to dig into these yet (only familiar with the misfire codes) but I thought I'd post in case there's something that stands out to someone.
If rod knock can safely be ruled out, maybe I should make a new thread without it in the title for more visiablity?

Thanks again for the help!

 

Also, when I pulled the coil packs, #1 had brown splatter on the rubber tip. It was baked on and didn't rub off with my finger. Cleaned it with some water and a cloth, and let it thoroughly dry. It was from the same cylinder that had the rusted in spark plug from back when I bought the car a few months ago. There is still some visable rust present around where the spark plug screws in at the bottom of the socket. Not sure how to deal with that.

Coil #3 had sort of white stripes (maybe light burn marks?) on the inside of the tip. The thing is they were evenly spaced all the way around. Could it be carbon tracking?

No visable cracks the rubber parts. I wasn't able to pull out the plugs because I didn't have a socket.

I rotated the coils to the right. I'll have to drive it a bit to see if the codes change.

 

Yeah, my above comments are still waiting for mod approval .

But to clarify, here is a recap of the timeline as it pertains to possible water damage:

- March 2022: The knocking/shaking starts - with no warning - immediately after fueling up (water in gas?)
[Also possibly relevant?: This happened after driving from the NE (below freezing at the time), to SE, where it was
60-70 F, in two days. The previous owner had the car in the NE prior to this.]
- After a couple days, I check cylinders and discover condensation on coil pack #1 (and a little on either 2 or 3, I don't recall)
- Spark plug #1 is rusted in bad (had to an extractor socket to get it out). So obviously water had gotten in there before all this too. Could be due to the missing fender liner on the pass side (same side as cyl 1).
- Put in new plugs and swapped coils. No change.
- Checked coils again a few weeks later. No moisture.
- Checked in coils now (4 months later). No moisture, but... as I said above:

Adding pictures for reference:

Mysterious brown splatter baked onto COP by random_username posted Jun 25, 2022 at 10:30 AM

Rustycylinder1 by random_username posted Jun 25, 2022 at 10:42 AM

Coptip by random_username posted Jun 25, 2022 at 10:42 AM

 

The wells have been dry each time I checked after discovering the problem, but I'm going to work on getting more of the rust out of #1. No oil present, so I think the gasket is okay.

Was actually looking into this today. Found this TSB on the forums. Linking here in case someone needs it in the future.

I'm going to seal the joint in the middle like it says, but I'm wondering how best to seal the weather strip that goes across the whole thing. I can move it up with my finger (I didn't want to mess with it too much) so I can't imagine it's creating a very good seal. Any ideas?

Any guidance on doing either of these procedures? I haven't messed with the ECM before, and what do you mean by "to spec"?

Thanks for chiming in, btw

 

The other update from today is that I started the car with each coil unplugged, one at a time, and the engine stalled for each of them.
Am I correct in assuming that means they are all functional?
And if I suddenly got codes for 3x cylinders, plus random misfires, is it even possible that all of them failed simultaneously? What might cause that?

Also confirmed the battery voltage is low (I'm assuming code C1241, from the list above). Tested after car had been parked overnight:
11.9 unstressed
11.6 stressed
14.3 charging
Not sure if it relates to the rough engine though...