I asked the same question a few months ago, I forget if it was here or in Probetalk. I don't remember the specific but it's definitely possible. Since all the Miller cycle engine is is a souped up KL3 with a supercharger and intercooler, all you need is more room. Specifically, you need to do some custom hood work in order for it to clear it. i don't know about the tranny but it might require some work since it was designed for an ATX.
The thing is, for the cost of a Miller Cycle engine, plus all of the modifications needed to make it fit properly, you could have spent half as much on a KLZE that pumps out the same HP.
I was seriously thinking about doing this swap until I started looking for prices for the Miller Cycle. First of all, since they are rather new, it's incredibly hard to find one that has not been totalled. Then if you do find one, you're not going to get it for under $2500, at least not the ones I've seen.
That would be a helluva mod huh.... Imagine getting a KLZE and then using the SUpercharger and intercooler from the Miller Cycle on it..... Ohh kids....
One of the biggest problems with this swap idea is underhood space. The Miller motor's intake plumbing is quite a mass atop the engine. Go to a Mazda dealer, take a measureing tape and pop the hood on a Millenia S and measure a few points (e.g. from the top of the valve cover to the top of the intercooler...) I can see some ugly hood mods to get it to fit that way. Width-wise (front to rear) the motor may have some interference problems with the firewall.
Also, the engine mount near the front of the engine (i.e. where the belts are) is quite different than the mount used on the other KL motors to make room for the blower drive belt.
A manual, AFAIK, was never bolted to the Miller motor but the block is pretty much the same so an MTX should mate properly. I'd assume a KL03 or KL08 flywheel would work.
Also, I noticed one day while drooling over a Millenia S that the tach shows a redline of 6000, not 7000 like the other K-series engines. This might be because of the blower but is certainly something to think about when driving spiritedly with an MTX
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