Notes from engine swap and battery reconditioning

Hey guys, I recently swapped in a "low-mileage JDM" motor and reconditioned the hybrid battery in my 2013 Prius, and I thought I'd share a few notes from the process. There are a million guides for these things out there, so I'm going to focus on stuff that isn't in most of the guides.

Three years ago, the head gasket in my Prius let go, and I kept driving it while I figured out what to do about it. It would knock a bit when I first started it up, and occasionally while driving, but then it would clear up and run fine (aside from steadily eating coolant). Well, one day my wife was driving the car with my infant daughter in the back seat, and it decided to throw a rod in spectacular fashion. It tore a hole in both sides of the block, did some damage to the head, and when I pulled off the cover under the engine, bits of piston and connecting rod fell out.

I kind of wanted to convert it to a full EV - I figured it would be a good candidate for such a project, because it already has a bunch of electrically-driven accessories. I had a bit of a chicken-and-egg problem with figuring out the CAN-BUS protocol to control that stuff though - I needed a working car to suss that out. So I let it sit in my driveway for three years while I focused on other stuff, until finally last year my neighbor was selling their house, and I decided it was time to get it out of the driveway. I was trying to figure out if an EV conversion was within my capability (using an EM57 motor/inverter/PDM stack out of a Leaf, a ZombieVerter VCU, a Bosch iBooster brake booster, and a DIY 25kWh LiFePO4 battery pack with an Orion BMS 2), and while I was shopping around for parts, I saw an ad for a "low-mileage JDM" engine for $900, and pulled the trigger. That was a lot cheaper than the prices I was looking at three years ago, and the motor had lower mileage than the ones in junkyards here.

I don't actually know what the mileage was on the motor I got, but it was definitely clean. The spark plugs looked barely used, and I didn't even need to clean out the EGR cooler. It ended up being $1250 shipped to Indiana.

I've never done anything like this before, but it wasn't too bad. I was able to do it completely by myself, though it would have been nice to have a helper when I was sliding the new engine in. I had some extra-long M10/1.25 bolts that I'd gotten to use for hoisting the engine, and I used those temporarily in two of the top engine-to-transmission bolt positions to grab the engine and pull it in. Then once it was close enough to get the regular engine-to-transmission bolts started, I pulled the long ones out and replaced them with the proper bolts.

You don't see this in any of the youtube swap videos, but I found it easier to get to the hoses and stuff on the right side of the engine with the inverter wires disconnected and moved out of the way.

The purge line on the JDM motor has a narrower diameter than the USDM one, so you have to swap the ones from the USDM motor. You can see a bit about that in this video:

Being a person who was not versed in engine swaps, I didn't realize that the guide pins are supposed to be in the engine. When I pulled my old motor out, one of the guide pins stayed with the transmission. I didn't realize it wasn't supposed to be there, until I was sliding the new motor in, and it had a pin in the same place. Fortunately I was able to yank the old pin out of the transmission, without having to pull the motor back out again, by locking a pair of vice grips down on the pin, and then prying on the vise grips with a crowbar while rotating them up and down.

Trans-guide-pin by Eriol posted Jan 22, 2026 at 10:22 PM

The car had about 1/3 of a tank of fuel when it was parked, and I didn't want to even try to start the new motor with that old gas. I bought a battery-powered siphon on Amazon, but it turns out you can't siphon fuel out of a modern car - they have a ball valve at the base of the fuel filler tube, so that the gas doesn't run out if you roll the car over. I was able to cut a hose at an angle and get past that valve, but it kicked it off at an angle so that I couldn't get it down into the fuel. What I ended up having to do was disconnect the fuel line from the engine, ran a hose from it to a 5-gallon gasoline jug, and then hooked a bench power supply up to my fuel pump (under the back seat) to pump the fuel out. I wish I'd done that before I connected the fuel line to the engine. The old gas was actually clear and didn't smell too bad, but I didn't want to take any chances with it.

Running-fuel-pump by Eriol posted Jan 22, 2026 at 10:58 PM

When I finally got to first fire, the engine was bucking something awful. It sounded like a rod knocking, and my heart sank because I thought the new motor was bad after all that work. It turned out to be a misfire on two cylinders, though - the injectors that came with the JDM motor were fouled, and I had to swap the ones from my old motor into it. Once I did that, it ran fine. If I had it to do over again, I'd probably see if I could get the ones on the JDM motor cleaned and flow-tested before putting it in the car. 20 years ago I did that on my Supra pretty cheaply, there was a shop near the Indianapolis Motor Speedway that specialized in that sort of thing, but sadly they're not there anymore.

I also went ahead and replaced the motor mount, front struts, sway bar links, spark plugs, transmission fluid, and inverter coolant while I had everything apart.

I also reconditioned the battery - I thought, after 207,000 miles and then three years of sitting, the hybrid battery would be shot. It actually ended up not being too bad - most of my modules still had over 5,000 mAh of capacity, a few were down around 4,400, and one was down to 3,600. Not great, but it probably would have worked. I bought six cells from a guy on eBay, and I highly recommend him - you tell him the specs of your cells and he'll sell you ones that match, and he also sells nickel-plated steel bolts and bus bars, which are hard to find, but you'll want to use. His eBay name is "carsandcards04". The cells he sold me were actually better than what he promised. I have no affiliation with him, it was just a pleasure doing business with him, and I was glad I found him on eBay.

A note on the bus bars and bolts - you actually want to use nickel-plated steel, not stainless steel. The studs on the Panasonic modules are nickel-plated steel - you can tell by the fact that a magnet will stick to them. If you use the stainless bolts that everyone sells, you risk galvanic corriosion. The stainless steel bolt will be more noble than the regular steel stud, so the stud will corrode. Maybe it doesn't matter a lot, because by the time it becomes a problem the car will be old as hell anyway, but if you're going to all the trouble to recondition the battery, you might as well do it right. It's hard to find the right ones, but the seller I mentioned above has them.

Stud-magnet by Eriol posted Jan 22, 2026 at 11:02 PM

Nuts-magnet by Eriol posted Jan 22, 2026 at 11:02 PM

Charger - at first I bought a ToolkitRC M6D off a recommendation I saw somewhere, and it might have worked, but it didn't support setting a capacity limit, and from memory I think the time cutoff was too short too. So I went back and bought a new version of the CQ3 charger that everyone recommends, the "BGAUD" one, and it did the job. It doesn't come with alligator leads, so I had to purchase a set of four XT60 female to alligator leads separately.

It is a time-consuming process - I think it took me 2-3 weeks, only being able to fiddle with it before staring work in the morning, and at night after the kids went to bed. Then I had to wait for the new modules to arrive, after I determined how many I wanted to replace, and then I spent another day testing those to make sure they were OK. I didn't load test the modules, because I was so constrained for time, but the pack has been working fine so far.

One final note - if you're about to do something with a car that's been sitting for a long time, check the cabin air filter *before* you turn it on and let the fan run. Mice like to nest in there, or in the blower motor. I got lucky and there was only a small amount of mouse leavings in the filter, and no nests in the vents or blower motor, but there are horror stories online of people getting horrible noises and smells from their HVAC system, and finding a nest in the blower motor.

I did have mouse poop around the back seat, and I found one nest under the hump that the front passenger seat bolts to. The car didn't smell great, so I deep-cleaned and shampooed everything, and that took another week. I ended up getting an extractor head for my shop vac, and some pump sprayers, and shampooed everything with the P&S three-stage treatment. Now the interior smells nice, and I fully expect this car to hit 300,000 miles with minimal maintenance going forward.