Misfire issues

First, did you follow the factory routing for the spark plug wires? Use all factory standoffs and looms? Are the spark plug wires touching any metal parts?

Try this old racer's trick. Run the car in a totally dark location. Look for the blue hue of escaping spark. Inspect the wires for white spots which is evidence of arcing. Arcing doesn't take very long to ruin a set of wires.

When was the last time the MAF was cleaned? PCV value replaced? Fuel filter replaced?

Also, excessive EGR flow can cause this symptom. Try disconnecting and plugging the EGR vacuum line. Does it improve?

Just wondering if you understand that with today's high energy ignition systems that IF the spark plug wires touch metal objects and arcing occurs, this will break down the insulation and ruin the wires. So if damaged, simply correcting the routing will not fix the problem. Further, it really doesn't take log to ruin a set of plug wires if arcing occurs.

It's important to understand this because as you post back, the assumption made is that all of the previous items have been ruled out. Therefore, each trip back to the well is likely to get more esoteric possibilities. The resultant wild goose chase is a waste of time and resources.

Your problem could be arcing to #3. Just checking for spark does not rule out arcing. Further, it would be expected that a marginal spark plug wire would be more likely to misfire under increasing load.

Since you stated that a few of the clips were broken, this brings up the possibility that a bad spark plug wire is the source of your problem. Consider replacing it.

In answer to your question about the check engine light. The light blinks when a misfire is actually occuring. If engough misfires happens that emissions levels are no longer being met, the check engine light is "latched" and the DTC code posted.

Have you done the EGR test?

Just my two cents worth if you haven't figured out your problem yet, but couldn't a bad (or one going bad) coil pack possibly cause a misfire occasionally?