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From what I have read on here, a swap from a 92-93 Probe or a 91-93 MX6 is the easiest swap to do. I would need the engine, the ECU and the air thing AIF(?) I know there are other things I would want to upgrade like the exhaust etc but I like the fact that all of the sensors and wires are a direct bolt in. My goal is to find one in the junkyard with clean oil on the dipstick and a car that was totaled. I will probably go ahead and change the timing belt, water pump and change all of the gaskets too. I might even take the heads off and do a little porting of the heads too and put in thinner head gaskets to bump the compression a bit.

There's sort of an ongoing debate. Some people think it's best to get a cheap junkyard KLDE as you suggest. The price is good, it's a direct bolt in and 40hp increase.

There are others...myself among them, who disagree. I would much rather spend a bit more to get a KLZE from a respected engine importer which bolts in exactly the same, has a lesser chance of being total shyte and will net you 70hp increase over stock.

Your years are wrong, its a 93+MX6 And Probe and 626 and 95+ Millenia.

The 88-92 MX6 Didn't have a v6, and the one in the same generation Probe used an incompatible an aniemic 3.0l vulcan v6.

Don't forget you'll need a clutch. Your oem clutch is only designed to handle 115ftlbs and is worn, the 2.5 will make 165ftlbs

I totally agree with wytbishop like, for a few more dollars you get a much lower mileage and more powerful motor you know. You could totally do it the way your talking like for sure but if you do decide to go KLZE remember to source out a KL31 or Kl36 ECU as well right.

KLDE, Jap KLZE, Milli 2.5, are all equally 'easy' to swap. There's no real brain busters in any of them. Its basically up to how much you want to spend and how much you want out of it.

A KLDE doesn't fall on its face in front of a ZE, it just tires out up top a little.

Its actually funny seeing i spent 3 weekends doing ym ZE swap. I NEVER even thought it'd be that easy seeing i did it all myself. Take a lot of pictures if your memory is bad like i did and really, its easy.

Cheapest route is
KL-DE engine preferably from an automatic car at the wrecker. Find a car where the body is f'd so you know the engine is good. Buy the engine, air flow sensor & ecu. MAKE SURE THE ECU IS 93-95 that is OBD1 (if you're car is 92-95).
Should cost you under $250 for it all if you have a wrecker where you can pull your own parts.
Thats the best route, use your flywheel & you can snag an exedy clutch off ebay for $100.
Then its just fluids...
You can do the swap for under $400 with a new clutch.

And yea a KLZE does make more power (pretty much just after 5.5k ish rpm) they are a crapshoot you never know how they were treated & how long they have been sitting (maybe ten years) without oil in them drying out all the seals etc...
Its a decent argument, I guess the most ideal option is get a klze & recondition it & of course yea buy a KL36 ecu for at least a couple hundred bucks & use your stock air flow sensor.
If you get a j/y klde you can look for one that somebody did maintanence on (valve cover gaskets are usually a dead giveaway) you can even take the oil cap off & see if its still bronzy looking in the engine or if they went too long on oil changes & there is burned black sludge in there.
Anyway difficulty-wise they are all going to be the same, I guess the US spec millenia is harder cuz you have to swap water jacket output pipe. Just small stuff really, either way the vacuum lines will be different on them all.
If emissions is an issue & you need a functioning egr be careful getting a klze because you may have emission problems depending on how you install it.

Do the stock DE manifolds line up with the MX-3 Y-pipe?

I'm pretty sure they wouldn't...point being no matter what engine you install you'll either have to redo the exhaust or use the K8 exhaust manifolds and reuse your stock exhaust system which will rob significant power.

Best bang for buck IMHO...

KLZE curved neck engine...do your best to ensure you get a good one...$600-800ish
Exedy clutch...$100-130
Used Probinator ECU <$100 if you can find one. More if you have to buy a JDM ECU
Exhaust...mine was aobut $500 but I went the deluxe route. You could do it for $250.

When I did mine I did everything. New motor mounts, timing set, water pump, oil pump, belts hoses, plugs, exhaust,...everything and it cost me a lot. You don't need to do all that, but I personnally don't think you can really do a good engine swap for $500. You're just asking for trouble down the road. It'll cost you more in the long run.

I haven't spend a dime on my engine except for oil changes since I did my swap.

Stock DE manifolds do bolt up.
If you get a millenia engine you have higher compression & ZE heads. You can add (if you want a little more power) colt cams ($350+) or klze cams for $150ish

Its kind of like this wyt. AS I SEE IT*
What is better at this point higher mileage 120kish a feasible find , on a motor that has been driven & had oil moving around in it.
OR an imported JDM engine that may have been sitting dry of oil for 5-10 years (big turnoff) & thrown around on a boat & transporting containers etc... I have blown plenty of klze's over the years but I have had the most luck with junkyard motors over imported engines. I have spun way too many bearings on klze's. Look on probetalk people fry klze's all the time.
They are the most power but honestly there is no gaurantees anymore. If you are going klze IMHO I think reconditioning from the bottom up would be your best bet.
Its your car & you can choose really to go cheaper or to go all out.
I will add this though, Alot of pull it yourself wreckers offer an additional 1 year warranty for a small fee. Typically JDM importers will only offer a start up or 30 day warranty sometimes no warranty (& forget about cashing in on a warranty with some of the sketchy importers out there; recommend read some reviews before buying from them you'll see)
I could go on & on about the comparisons...
Ohh yea you are right about the $500 mark I guess a timing belt kit & water pump may put you over $500 on a junkyard KL swap.

IIRC the rear manifold is different, the bolt pattern for y pipe flange is indexed slightly different. same diameter and geometry etc as Mx-3, so just use a matching manifold/y pipe combo. Also DE y pipe is about 6" longer than stock MX one.

Or, $150 -> Egay headers.

I drove my KL with K8 exhaust on it, the ebay headers and 2.5 basically straght thru did make a noticeable difference over 5000 rpm.

For what it's worth, my '93 has a Milli KL and a stock K8 exhaust. Pulls as hard as the only other KL car I've driven, which was a 99(iirc) KLG4 626, up until the higher RPMs. You certainly won't complain about the low end with a K8 exhaust on.

Truth is your budget makes a lot of decisions for you. Do the best you can with what you have to work with.

My budget made me wait 2 years, and I'm still waiting. I set a $5,000 budget for intake/engine/exhaust build... I'm only about $800 into it, and have a looong ways to go.

That is a $125 junkyard motor:






This is a $900 jdm klze:


*note that this is a picture of how the engine came to me straight from an importer

yep, if you have the time and a little know how then you can definitely make a more informed decision if you know what you are looking at. glad my KL doesn't look like that inside...