Vibration Problem Recommendation with CPO

Just got my 2000 996 C2 back from my local, reputable indy shop (Monaco Motors, they are fantastic!) for a clutch and flywheel repair amongst other non-warranty consumables [sparks, trans fluid, etc]. I asked them to see why my passenger seat vibrates so much at idle and when driving. They said that it could possibly be the flywheel, but the problem still persisted after the flywheel was replaced and the new clutch installed. Although I only noticed the vibration in the passenger seat, they found that the vibration was affecting the whole car. Gene their Porsche tech said that the engine mounts were another potential cause of the vibration. He said that after changing the mounts, if the problem still persists it could very well be the motor itself. The car's CPO warranty ends in October, and I cannot afford to replace the motor myself if that IS the problem and want to iron out all the kinks prior to the warranty expiring. Funny thing is I asked the stealer about this, and they tightened the seat bolts, instead of bothering to find the root cause. Can someone recommend a course of action, and what potential impediments I would possibly face with the dealer? Has anyone else had this issue?

How many miles and were any codes read from the DME?

52k, 34k when purchased. The mechanic didn't hook the DME or read codes, but if the computer hasn't alerted me (the lowly driver) to anything suspicious. Thank you kindly Doug for any further thoughts on this.

My seat vibrates also. Never tried to find out why.

I've heard some people claim that smoothing out their idle removed some vibration from the seats. They are usually discussing cleaning the MAF or new plugs.... I'd check of for a misfire code on the computer.

Took it to the Auto Gallery in Woodland Hills today (local dealer). They said I would have to put my stock exhaust and intake back for them to further diagnose. Which I read as "we are not interested in finding what the problem is." Maybe there is no problem, but when a reputable Porsche mechanic says "it's not normal" and my warranty is running out, I get nervous. Oh well... thanks for the replies.

The reason they asked for you to put your stock parts back on is that Porsche will void the warranty if there are any aftermarket parts on it. I think the guy was telling you something without saying it. The subject of warranty coverage and aftermarket parts has been discussed extensively....you can search for the discussion threads....but the bottom line is that "technically" Porsche can void a warranty if an aftermarket part can even remotely be connected to the problem. I have a vibration in my TT that started after I installed a Europipe system...Up to this point the vibration has been diagnosed as a throwout bearing going bad, maybe a clutch plate....possible motormount issues, and finally...a vibration caused by the exhaust system causing the vibration as it hits a certain decibel rating...in my case right at around 3800-4000 rpm. I'm beginning to think that the db suggestion is the issue....because the other possibilities should cause a vibration at any given speed or rpm. The difference here is you only feel it in the passenger's seat...I feel it only in the clutch pedal. That would suggest a different cause....but I'd look at the body under the passenger's side of the car and look for something like a hard line rubbing or vibrating against a clamp, motor part, or exhaust.