If you were to drop the tranny and inspect your flywheel, I would bet you could see discolored spots throughout the contact patch of the flywheel and if you didn't replace the pressure plate, it as well. The spots can be streaks, blotches, and spots, typically the size of a BIC pen or larger (see image below for example). These heat spots are a sign of guaranteed warping in the flywheel surface and/or pressure plate. Take it to any automotive machine shop and they can resurface and rebalance it. As long as any surface damage to the clutch disc or pressure plate is repaired (the PP will show the same damage as the flywheel and should be either machined or replaced at the same time as a clutch disc as well) it should cure 100% of the shuddering until you overheat the clutch repeatedly over time.
Machining both parts should be less than $50.
Example image of overheat damaged flywheel/pressure plate surface.
Needs resurfaced at autmotive machine shop or replaced.
Thanks to AllFordMustangs.com for the above image.
Image of a fresh surface
Thanks to NorthWestOffRoad.com for the above image.
***HINTS***
Touching the surfaces of the clutch disc, flywheel, or pressure plate during installation can cause hot spot damage like the first picture. All surfaces should be fully clean of any form of contaminant.
The damage naturally occurs most often when you touch the throttle two or three times as you take off, altering the RPMs of the engine up and down irratically. Some think it sounds cool, but it has consequences, overheating the clutch. If you note at the right and left of the first picture, within the contact patch for the clutch disc, you can see two hot spots that "match" each other. Those are marks from the holes in the stock clutch disc. When revving the engine multiple times during a take off, it creates added friction and heat. Then once the clutch is released, the flywheel, clutch disc, and pressure plate are all sandwiched together, not allowing the heat to escape (most likely during long hard accelerations) causing the heat defects and warping the surface.