Well my 03 Type S M6 needs a motor. Only one cylinder has normal compression and the rest are all over the place ranging from 270 to 105 psi. I will eventually rebuild it but for now I'm going to throw in a used one.

From research I know the auto motors and manual trans motors are different and don't directly interchange. Anyone know if the differences are parts I can easily swap from one motor to the other, or is it more involved than that.

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i think you'd be better to grab a used MDX or odyssey motor and use that bottom end. Then put your CL-S heads (and everything else above that) on.
Info here: https://acurazine.com/forums/showthr...=714305&page=5

Also here's a page with info on what has to be swapped from the manual motor to your auto: https://acurazine.com/forums/showthr...p#post13583818

 

I did a swap auto engine to manual cl but what gnuts said is very good idea if you plan to keep the car. I sold it and now I regret it that I sold cl and didn't do 3.5...

 

Curious to hear why, if you want to elaborate?

 

I'd buy a lower mileage j32a2 from an auto off car-part for 400-700$ (lower mileage) and swap the two sensors necessary (15min work) to make them 6mt compatible. Done

 

Ended up finding a 03 auto motor with 58k for $760 shipped on Ebay. The 3.5 swap sounds interesting but I am sure the pistons in the 3.5 shortblock are set up for lower compression and what about tunning it properly after I am done?

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My wife is gonna hate you guys. Looks like I'm gonna be rebuilding and stroking the CL-S motor once I get it out. All I gotta do is find out how to tune it. Car has to pass emissions so I cannot go stand alone.

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From what I've seen these motors are usually pretty bulletproof. How many miles on yours for it to be worn out? Local junkyards around here sell the motors for less than $500 as they're over stocked on them. Did your car get low on oil or something at sometime?

+1 on the 3.5 block swap. Pretty straight forward from what I've read.