Drive line roughness after new clutch install

I have a 96 cobra with 88000 miles. The clutch went out and I had a motorcraft '99 11" clutch kit upgrade installed this past week by a local transmission shop, picked it up Saturday. I like the clutch, seems like half of the pedal effort of the stock clutch. BUT, driving around today I noticed a roughness at 1100rpm as it drops down from reving it up, hangs a bit and seems to shake some, then smooths out as it drops to low idle. But worse, from 4000rpm up its really seems a lot rougher than I remember. I don't know that much about clutches but it seems like something is out of balance. Could the replacement flywheel be out of balance? Does the shop need to do something to balance that at install? What else could have gone wrong? Something with the driveshaft? I could use a few guesses to take back to the shop with me. These guys have been around a long time, which is why I picked them, but it would be nice to have some learned opinions as backup when I discuss this with them. Any thoughts GREATly appreciated. Thanks Mike

Lo Pony said:

They're supposed to index the pressure plate to the flywheel - there's a yellow dot on the flywheel and a yellow dot on the pressure plate as supplied from the factory (or at least there should be).

Other than that, it could be unevenly tightened or the throwout bearing is more than one of the typical pieces of crap that we all have...

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Wow. That was one scarey article from the attached link. I guess I can only hope that the tranny shop I chose is willing to take the steps required to fix the problem without draining me dry and fighting me about it. I was considering changing pinion gears as a next step but I'd guess I'd better choose a little more carefully in picking a shop to do that, if I do it at all now. I did choose a shop that had been around for years, but there is another in town who claims a lot of experience with cobras, though they are priced well above the rest around here. Thanks for the timely reply - Mike