ENGINE 2.5L V6 (KL) (Last update: 01/23/2005)
Even after 145,000 miles (and 12 years of MY driving) the engine has faired extremely well with nothing but factory recommended maintenance. The A/C compressor and coolant pump have each been replaced once (at 60,000 miles) and the timing belt tensioners (at 120,000 miles). Otherwise the engine still runs like velvet. Why dick with something that ain't broken, right?
So, I don't plan to do much tinkering at all with the engine, except for one or two "low risk" modifications...
Outlaw Engineering ThermoBlok Phenolic Spacer Kit
To help keep the intake charge air temperature down and get a little extra horse power, I've added a set of Outlaw Engineering phenolic resin spacers between the engine block, the intake manifold, and the throttle body. Here's how they work.

Install time: Over 9 hours. Well... I did it by myself and this was the first time I've ever taken the intake manifold off of a car, so this was very much a cautious learning experience. I feel good just that I was able to put it all back together without any mistakes (except the one coolant hose clamp that I forgot to tighten). I also took the opportunity to clean the gunk out of the intake manifold and throttle body, and that took about 1.5 hours alone. If I had to do it all again, I feel confident I could complete the install in less than 4 hours.
You can see the spacers in the pictures below (circled in red). Even the manifold and throttle body bolts are thermally isolated with phenolic washers. As noted in the very well written instructions, this modification moved the throttle body far enough that the bolt holes in the throttle cable bracket on the back of the intake manifold had to be elongated quite a bit. A bit too much, actually. You can almost see how far it's offset in the upper left corner of the picture below right. I'll feel safer making another one from scratch to make up for the extra distance.

After putting the spacers in, I went for about a 45 minute highway drive and with the engine still running, I stopped to see how cool the intake manifold was. It was warm, but I could place my bare palm against it for a few seconds before it got too uncomfortable. The intake manifold is definitely running cooler.
Outlaw Engineering also claims that I could see a performance gain of as much as 8.7 HP and 12.5 ft-lbs torque. I took the opportunity to get a dyno run, but I had also added a high flow converter and catback, so I can't be certain how much performance gain I got from the spacers alone. See the dyno plot.
Outlaw Engineering Throttle Body Coolant Bypass Adapter
Along with the Outlaw phenolic spacer kit comes an optional adaptor to bypass the engine coolant lines going through the throttle body. This helps keep the throttle body (and therefore, the intake charge air temperature) cooler.

The bypass adaptor is shown above. The Stone IPA beer bottle is merely for size comparison. :-)
The bypass adaptor is a "fixed" bypass... which would be fine for San Diego, but...
... since I'm moving from San Diego to Washington D.C. in February 2005 (sucks to be me), I'm not sure that using the bypass adaptor will work well in the winter weather. Washington D.C. flips from damn hot summers to pretty damn cold (and wet) winters, so I'm investigating the environmental conditions needed for the moisture in the intake air to ice up inside the throttle body (major power loss) and decide if the fixed bypass is sufficient during the winters, or if perhaps a temperature regulated bypass valve could be used to allow engine coolant flow through the throttle body when icing conditions exist. See diagrams below... and please comment if you like the idea and/or have a practical means to assemble it. The diagram on the left shows the Outlaw Engineering "fixed" coolant bypass configuration. The diagram in center shows the temperature regulated valves in the "open" position letting warm coolant flow through the throttle body for winter conditions. The diagram on the right shows the temperature regulated valves in the "bypass" position, diverting the coolant and keeping the intake charge cool.

Meantime, I've left the bypass out.
AWR Motor Mounts - Polyurethane bushings.

Install time: Over 5 hours for the rear motor mount. Less than 1 hour for the front motor mount. The rear motor mount is a pain in the ass to get to. Gaining access includes removing the forward cross member, the manifold collector pipes (or header collectors, if you have them), and some cable bundles attached to the fire wall above the mount.
The V6 motor is oriented laterally, so the motor case will torque forward when adding load, and then to the rear as load is removed. The front and rear mounts are the principal mounts that retard this engine roll. There are side mounts, too, but they mostly act as vibration dampeners. The OEM front and rear motor mount bushings are made of rubber and designed so that the motor mounting points are actually suspended in air in the middle of the bushing. No wonder the stock MX-6 is such a velvet smooth car to drive.
The AWR front and rear motor mounts add a great deal of stiffness to the engine, and nearly eliminate the torque roll. Reducing the roll effect from torque also reduces the wear and tear on the transmission and reduces wheel hop on quick starts. The unfortunate side effect is that you lose the soft ride. With the new mounts, I now feel a significant increase in the engine vibration through the steering column the driver's seat. The car almost resonates and sounds like an earthquake or echo chamber at lower idle speeds, so I may need to adjust my idle up a bit to avoid the noises and resonance.
I may also decide to just buy a new set of OEM motor mounts. I liked the car when it was smooooooth.