This one is going to be difficult to diagnose.
The transmission shudder is very similar to a misfire, especially when it's not severe. Some describe both conditions as driving on little ripples in the road.
Yes, plug wires and Coil Packs could be the real culprit however, being that the condition only manifests itself at those 'under-load' shifting points, a Dyno test may be the only way to nail it down, until the problem gets really obvious.
Every 30k to 40k miles you need to flush and replace your Transmission Fluid, including cleaning the pan and replacing the Filter. Regardless if you're having any problems, this is required maintenance. I've thrown that into this conversation because, the Transmission shudder that plagues these cars is kept at bay when we keep our transmissions clean, at the recommended intervals, with the recommended fluids. Most of us also use some kind of name brand additive as well,
Lubegard is the most recommended. The shudder can be mistaken for misfires, and it does occur during shifting.
An OBDii Scan should also be done to check for intermittent, stored, error codes. This could identify a misfiring coil pack, dying fuel injector, bad spark plug wire, etc when the condition isn't constant. A constant problem (error) would cause the Check Engine Light to remain lit after the engine is running.
Have a look at your miles, keep in mind the service interval for trans. fluid flush, take the steps required, check for stored OBDii codes.
We have a few Conti owners that live with a similar problem, no-body can figure it out, one of 'em recently traded the car from frustration.