I've owned my 1999 M6 since 2003 and the drive train used to feel very smooth throughout the RPM band in stock form. Ever since I started with internal engine mods there's a vibration that permeates in the car around 2K-5K RPMs. I've racked my brain for years trying to figure this out and I've noticed other members on the forum that experience the same issue and don't seem to get resolution. The vibration can be felt in the drivers seat and felt in the shifter. The only way I know how to describe the vibration is a pronounced "lumpy" feel that occurs about twice a second and speeds up as the RPMs go up. Nearly every drivetrain part has been replaced at one time or the other with no change in the vibration. Below is what's been modded and the approximate timeline:

2004 - Long tubes/X-Pipe/Cat Back (no vibration from this)

2005 - Moderately aggressive cam, ported heads, SLP aluminum flywheel/clutch/PP (vibration started here), new master and slave

2006 - Installed aluminum driveshaft coupler in the TT (front coupler only)

2009 - Installed an LS3 (engine was balanced) w/ a moderately aggressive cam, A@A SC, and moster stage 3 flywheel/clutch/PP new master and slave, poly engine mounts; removed the front aluminum driveshaft coupler and replaced with the stock rubber one (no change in vibration)

2010 - Installed a Z06 torque tube (no change in vibration)

The only thing that seems consistent is an aggressive cam and a non-stock flywheel. Will a lopey cam cause engine vibrations?

I've read that GM takes extra care in balancing the M6 models. Is there a way to replicate the GM drivetrain balancing process?

 

You've answered your own question. It started when you installed the clutch assembly. That's where I would start.

 

If the problem began with the first clutch & flywheel replacement, then obviously the issue is related to that operation. Since the entire engine was replaced (I assume that none of the LS1 bits were transferred to the LS3) and the vibration did not change, then that would suggest that something in the driveline was bent/damaged/misaligned when the first clutch & flywheel was replaced and this issue did not change when the LS3 was installed

For starters, were all of the dowel pins present and accounted for? Are you using an OEM guibo joint that is in good condition?

Some clarification would also be helpful. When do you feel the vibration: driving down the road, driving with the transmission in neutral, driving with the transmission in gear and the clutch disengaged, sitting still while revving the engine? Can you reproduce the vibration with the rear wheels in the air?

FWIW, even though the engine is internally balanced, I have seen threads indicating that flywheels had to be match balanced when replaced, in order to prevent vibrations.

I am familiar with one manufacturer that bolts the engine and trans together and runs them on a stand prior to installation in the vehicle. They add weights (bolts) to the flywheel to balance the entire assembly. When replacing flywheels, it is necessary to transfer the bolts to the new unit. ** I have no idea whether GM does anything like this **

 

1. All of the internal engine parts were replaced. Since this all started the torque tube and flywheel/PP/clutch have been replaced.

2. All the dowel pins are accounted for and installed properly. The OEM guibo joints are being used and in good condition.

3. The vibration is most often felt while driving. Gears 1-4 have the worst vibration. If driving in 4-6th gear around 1,500-2K RPMs the car is smooth. Any down shifting to 4th, 3rd, etc. from city or highway speeds seems to exacerbate the vibration. The vibration is worst in gears 1-4 while maintaining a constant speed or decelerating until under 2K RPMs. Quick accelerations seem to reduce the vibration. With the clutch disengaged the vibration comes and goes from 2-4K RPMs but gets very bad above 4K RPMs. I haven't tried with the wheels off the ground.

The strangest part is during a cold start the car is almost completely smooth for the first 5-10 minutes of driving throughout all gears and RPM ranges. Once the car is warmed up pretty good is when the vibration is the worst.

Regardless that the engine is balanced and the Monster is supposed to be zero balanced I guess it needs to be balanced as an assembly. I haven't been able to find anyone that can do this.

 

Look into buying or lending an EVA (Electronic Vibration Analyzer) from Kent Moore. They were uses in GM Dealerships to locate vibrations and also have a feature to balance the complete assembly. I have one of them and am in the process of trying this out. You basically determine the vibration frequency and use that to balance the engine/flywheel with a strobe. Pretty slick setup.
Search ebay and you'll find them.
Good Luck,
Alex

 

The strangest part is during a cold start the car is almost completely smooth for the first 5-10 minutes of driving throughout all gears and RPM ranges. Once the car is warmed up pretty good is when the vibration is the worst.

You said you replaced the torque tube and FRONT coupler. Have you replaced both couplers? If it was the clutch ,it would vibrate cold or hot.

Here is my thought. You have a bad coupler that is made out of stiff reinforced rubber.
It holds it shape better when its cold and stiff. After 10 minutes of run time it gets warm and loosens up a bit allowing it to run out of balance.