Fore/aft cleat placement (which is a matter of how far your knee and hip extend, which muscles are bringing you power and what's going on in your ankle) can often benefit from an expert eye and measurement.

Side/side and rotational alighment are more, if they're off, they're torquing your knees every pedal stroke. You can feel that if you pay attention. Find someplace you can spiin steadily, preferably a reasonably flat road. Have whatever tool you need to re-position your cleat accessible. After you've warmed up, focus on how your knee joints feel. Does it feel like your tibias are being pulled to the outside or inside of your knee joints? Uncomfortably turned? A lot, or just a little?

Reposition your cleats (I always have to think way too hard about which way everything has to go, since my shoes are upside down when I'm moving the cleats ) and try again. See if that helps.