It is possible to install the 8-7/8" non-Turbo clutch disc onto a larger Turbo flywheel, but not possible to install the 8-7/8" non-Turbo pressure plate onto the larger Turbo flywheel.
Therefore, if no other parts were available at the time of install, the original Turbo pressure plate would have to be reused, which is a bad idea: You should never install a new clutch disc up against used surfaces. For this reason flywheels are resurfaced and reused, but no one resurfaces pressure plates, they are simply replaced. A clutch works by friction and pressure exactly how disc brakes work ... and you would never install new brake pads onto used rotors unless you first resurface the rotors. Otherwise the new brake pads won't break in properly, they will overheat and form glazed hot-spots which will cause high frequency vibration ( = brake squeal/noise) and decreased braking performance. The same is true with your clutch.
If your truck came to your mechanic with a high mileage Turbo flywheel & clutch kit, and he went to install a non-Turbo clutch kit, and had no other parts, then his only option would be to use the (smaller) non-Turbo clutch disc with the (larger) Turbo flywheel and (larger) Turbo clutch pressure plate. Physically this is okay, the non-Turbo disc will fit amongst the larger Turbo components and would function just fine. However you'd expect no mechanic to do this for the following reason: The pressure plate is a high mileage part. The flywheel is okay, as he would have resurfaced it, but pressure plates are not regularly resurfaced, other aspects wear such as the fingers that contact the release bearing, so a new pressure plate is
always supplied in a new clutch kit to replace the old unit.
If this is what your mechanic did, installed only a new & smaller clutch disc and reused the other components, the clutch would still work but I suspect you'd get chatter, it would certainly overheat and fade more regularly, and have a lower load holding ability than what it was original rated for. You'd also experience accelerated disc and pressure plate wear because the contact area would be reduced. Practically speaking, after some 20,000 miles you'd have one low performing and messed up clutch kit on your hands that would overheat easily.
Assuming the clutch was adjusted properly, this would however have NO affect on your transmission's shifting performance. The only way for a clutch to affect the shifting is if it was unable to fully engage. Then you'd always have a load on the transmission input shaft and
this would cause shifting issues. But this is not to be confused with a
bad transmission. Internally and by itself the transmission may be healthy but have poor shifting simply because it is not able to become fully disengaged from the engine. I hope this makes sense. You cannot shift the transmission when it is under a load (ie. accelerating). This is in fact why a clutch is needed.
To set doubt aside, the thicknesses of both the non-Turbo and Turbo clutch discs are the same and the hub that engages the transmission input is in the same position. So the transmission doesn't know what clutch kit you have installed apart from a difference in the moment of inertia of the clutch disc when the clutch is engaged.
To answer your question about shifting performance, to have a new clutch installed and
operating normally for a few thousand miles only to later experience transmission shifting issues, I would not assume the clutch to be the culprit. I'd only consider the clutch if it itself began acting up (maybe it has developed a fluid leak?). I'd start examining the transmission to see what is going on. Check how much metal has accumulated on the drain plug since you last serviced it and check the condition of the shift seat and socket (we offer high performance seat & sockets here:
http://www.marlincrawler.com/tech/guide/heavy-duty-shifter-seat-installation). Unfortunately there aren't many external solutions to a poorly shifting transmission. If the gear oil does not indicate excessive metal and the seat and socket do not help the situation, the only way to know what is going on is to open it up for inspection.
Best of luck,
BigMike
