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earlier this year I began an engine swap on a 2004 CRV 5spd and I wanted to clear up a few things I had trouble figuring out before I started. The engine was a k24a4 out of an 05 accord, the k24a1 that was in the crv had a bad oil leak from the oil pressure sensor port, there was a about an inch long crack starting at the threads of the sensor. anyway I pulled the engine and trans out the top with no real issues.
I decided to play it safe and swap timing cover, valve cover, oil pan, and of course intake and exhaust manifolds. pretty much all the major stuff, Using rockauto.com I began to cross part numbers of the various sensors on the engines to see what I needed to swap over, there are two VVT solenoids (you guys might call them something else) the one on the back of the head above the oil pressure sensor is interchangeable with both engines however the one the slides into the timing cover needs swapped over from the old engine. I did not mess with any of the timing components, cams, cam phaser, chains, everything from the k24a4 I left in place.

Now to note a few differences between the motors. according to my research if you decide to swap a A4 into your car you cannot simply swap the A1 head onto an A4 block. the a4 pistons will make contact with the valves/head when you crank it over so you are committed to using the whole long block which is where most of my difficulties began. on the back of the head (above the transmission) on the a4 head there is a water housing that has the EGR built in whereas the A1 has nothing, I decided to cut out a block off plate out of scrap steel and remove the egr valve, the CRV didn't have an egr system so there's no point in leaving it there, at the same time there's a wiring harness that belongs in the same place as the housing so connecting various sensors like the cam sensors is kind of tight with that water outlet in place but its doable, looking on Ebay they make billet plates to remove that manifold but you need to utilize the outlet for the upper radiator hose to I opted to just keep the whole k24 housing there. moving on. if you looking at the k24a1 motor, to the right of the intake manifold you have the original upper rad water outlet, this part bolts onto the head however the bolt holes and the shape of the water passage does not match up so I ended up using a billet adapter plate like shown, it worked perfect. lastly you'll have to delete the factory air box, with everything shifted around theres just no room to make it work.
so far there has been no need to tune the crv, it seems to have adapted just fine, it does feel a little more quicker but that's comparing a 240k mile motor to a 50k mile motor so who knows

Sorry if I have the terminology on a few parts are wrong i'm not a honda guy but wanted to share my experience for someone that may need it. i'd really suggest trying to find a replacement k24a1 motor, there was alot of headache with making this a4 work,
 

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Wow, this sounds like a major project! Thanks for sharing the details. I'd bet alot of these kinds of swaps would not work, but you certainly found one that did. Impressive. Got any pictures?
 
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