2003 Prius Brake/ABS Issues

Hello all, I've been researching all this for a while now but have come to conclusion I need assistance.
I acquired a 2003 Prius about a month ago and I have been trying to get it restored to good working order. It had been sitting half a year or so, with the then owners running it once or twice a week to make sure nothing had gone wrong with it. I test drove it and everything appeared to be operational. The ABS light was lit and was told it was a wheel speed sensor code that they had checked at the dealership. Decided to go for it and clean it up, I started it up again there and got it home. Everything went smoothly for the hour drive back to base, parked and went in to store all the documents before looking harder into the car.
While I was looking at cleaning everything I stuck my head in the truck and realized there was a dampness on the carpet. I started ripping into it and found the spare tire was almost completely submerged in standing water. I quickly punched the drain plugs and started looking for other standing water, it was also in the battery tray area also and then looking around for the plug in there.
I was told the car needed a jump sometimes in very cold weather and I just expected that the 12v battery was a weak.
I went to start the Prius again and found myself hearing a noise that I would later come to find out was coming from the ABS ECU behind the glove box, and greeted with every warning light on the dash being lit. ABS, BRAKE, Red triangle, and check engine.
I tried to figure it out myself and have read every thread on here with people with similar issues. I found a few ABS fuses blown, even changed out the 12v Battery in it with no luck. I got the codes from the jumper method. They are 15, 51, 52, 56, and 64. From what I could find on a few of the codes, it is not getting proper voltage at either the ABS ECU or the linear solenoid. Even with fully charging the new battery with an external charger.
I got the leak under control, turns out they were using the small spoiler on the trunk to slam the trunk closed for a while and it rains up in the Northwest a ton. The spoiler had lifted up where the clips in the front are and had been just letting water strait into the trunk.
I had checked all the fuses and had found ABS 4 fuse blown but replacing it changed nothing. I tried to check the ABS relays but I couldn't removed them with by hands alone and decided it could damage them if I put a tool to it.
If anyone could help me with some info that would be amazing, thank you.

 

Yes! I got the info from techinfo.toyota com and spent a week trying to troubleshoot it. I gave up and decided to just sell it after trying everything but replace the pump. I went to sort it all back together and get it ready for sale and I just let it run for 30 minutes while putting the trunk back together, and the ABS, Brake lights, and the alarm just went off. Brake booster was working and even drove it around the block and tried some heavy braking with it. Looks like it just came back to life all by it's self.
I let the 12v battery charge a few times on the wall charger, and taking it out and putting it back in after was all I did in between it working and not. Going to check all the codes again soon. Got a M-vci and got it working so I should be able to sort out any issue it might also have.
Thanks for the help!

 

I thought it was the fuse, but I manually cleared the codes, when I did the lights and alarm stopped for about 4 seconds and then the codes 52, and 56 returned. Since they left on their own they have no returned. I looked again with the M-vci and they have no codes logged on the ABS system.

Thanks for the info Brian. I got the truck sealed, I removed all the carpet and trying to dry it out. Sadly I do not have a garage to dry it out. I'll be looking today at the buss bar, as I have 2 new codes, p3000 and p3030. I looked at the voltages on the battery. Block 18 was showing 0v so my only guess is the probe have failed. I think block 19 and 20? These one were reporting that they were at 20v.

 

Well sad news. I was out doing some errands and after leaving the Interstate as I was asending the off ramp. My dadh lit up with the Brake, ABS, and sounded the alarm again. No idea why it happened or how. Going to go get the codes and start throwing time at trying to figure out why it sorted it's self out and then returned after hardly an hour of driving today.

 

Update.
Got the codes back. New codes.
P1346 and P3009. I'll see what I can find. Thought I would let y'all know what is going on.

 

Well Finally getting back from work and getting ready to put some time into the Prius.

It is a 2003 with 260k miles on it. The poor door had a crack in the water channel for the truck, and the spoiler on the rear had been pulled off from the clips so there was gallons amount of standing water. Sadly this was not disclosed to me anon purchases else I would have declined the car. I've since sealed all the leaks, and have been drying to dry it out.

I got a used hydro booster pump assembly. Should be ripping into it tomorrow. I haven't had day light hours to work on it much. I couldn't find much info on P1346, just that it is a constant, and freeze framed code. I would think that it would run horrible if the timing lost top dead center. I'll see how hard it is to dig to the timing chain and see if the timing is still correct. I'm not sure if the Cam/Crank Shaft positions censors failing could throw this code or not.
Found out that in 09 the battery was replaced by Toyota. But couldn't find anything else about it.
I ripped out all the paneling around the trunk, and found corrosion around every bolt that wasn't Ones that bolted down the battery, looks like the humidity has got to the battery. Will be taking it out and looking into either cleaning the bus bar or replacing the tabs/probes.
Here is the freeze frame data for the two new codes. Note the negative amperage on the HV battery. Otherwise not a ton of data present. I'll be testing the p3009 tomorrow morning by clearing the code and doing the steps to see if it's in the battery or the Transaxle.

Thanks again.

 

Thanks Brian for the ideas. Your offer sounds temping, I live up in the Pacific Northwest and it feels like it never stops raining. I read that the 0v and 20v are a common sign of the voltage sense probe has failed on block 18. I think it's to do about how the computer measures the voltage between blocks. I am going to yank out the battery once I get the braked sorted out.

I got the old brake booster unbolted but ran out of day light before figuring out what way I wanted to get it out, either down below having to take of the passenger side drive shaft, or up and out with braking the AC lines. I've been debating how I wanted to go with it.

While I was digging around I noticed this and took a picture to share. My guess this might be my reason I'm getting a P1346 code.

 

Update.
I got the booster in and running. Bled the brakes with Techstream. Took a good 4 hours or so including tearing down and reassembly.
Removing the brake reservoir and associated hoses, plug, and plus a few bolts, gives you perfect access to unplug the pump assembly.
I removed all the connections for the main wire harness, and unbolted the plastic housing it rests in to pull it off to the side. I then removed the aluminum heat shield over the headers. I took the single fitting going from the top of the assembly to the rest of the brake system. Lifting the car up and removing the wheel and shroud, I got access to the 4 bolts that hold the assembly onto the lower plate. With those removed I was able to lift the old assembly up and out wiggling it pass the headers. It was tight between the valve cover and the AC lines, but squeezing the 2 sides of the remaining bracket and apply light pressure to the AC line, the assembly slipped right out.
Then it was as simply taking the bracket off the used replacement and doing in reverse of before. Went all in easy.

Sadly can't test to see if they are working 100% till Tuesday when the new crankshaft position sensor comes in. Also all the battery codes have vanished. but seeing I have a few days I might as well see about getting into the HV battery and see what is going on in there.

Thanks again for all the help!

 

Brakes are working great. The job was far simpler then I thought after all. After installing the new Crankshaft Position Sensor. I cleared the P1346 code. It came back as a pending code right away. Looks like the sensor being broken in half wasn't the cause. I'm going to look at the Camshaft Position Sensor to see if it's good.
I started listening to the engine run for a while and noticed it doesn't sounds like my friends 2002. There is a light ticking in the engine, I would have to get a probe and hunt around to be sure but it sounds like it's in the top end over by Cylinder 1. Now I'm wondering if the timing chain tensioner are failing or have become stuck. Looks like i'll have to look into the checking the chain visually.
I have yet to get the chance to take out the battery and clean everything/ replace the probe on block 18.

 

I thought I would give every one an update.
I spent more time finding leaks in the trunk, and finally was able to seal the trunk fully in. After that. I decided of the two codes I had still. p3030 and p1346. I would throw myself into the batter, finding and acquiring high voltage gloves, I yanked out the battery and replaced the voltage probe harness, and the Hybrid Battery ECU, and one of the plugs was showing some massive damage. Cleaned all the other copper plates and slapped it all back together.
Now with the battery sorted out my battle with the p1346 started. Still trying to sort it out.

 

As far as I can tell the P1346 is the ECM sees a dependency between the Crank and Cam/VVT-i position sensors.
I started by replacing the Crank position and Cam Position sensors. Then the VVT-i solenoid, also called VVT-i oil control valve. Still nothing.
Last night I started up techtream and started probing though data to see if I can find something other then tearing down to see if the timing jumped. I found that there was an active test for the VVT-i (bank 1) system and attempted to test it. Even though all the parameters of the test where satisfied it would not test. I'm unable to shut off the VVT-i system from techstream, it simply is locked in an On position. I installed the old solenoid and same thing, no testing. So I went to my father who owns a 2002 and tested his. Sure as shit, his tested fine.
Went back to my 2003 and started digging around with Techstream and found that the ECM has no VIN and has stuff missing that should be there. Also won't allow me to input a VIN as it says it is not the one stored. I'm thinking the ECM is damaged, I can do the tear down and test the timing. But the service sheet in the book just says check timing, if correct replace ECM.
After everything I've done to this car this might be the hardest repair so far as my M-vci can't reprogram ECU.