So I have successfully installed the om617 in my yj with a couple issues.

Two questions, why is there a clicking noise from my transmission. At first I thought it was the exhaust gasket leaking making that clacking noise but after replacing it there was no change.
The noise is coming from the clutch area. I did install a new clutch flywheel pressure plate and throw bearing when I did the swap.

Second why when I hit higher rpm it shakes but only under load. If I have the engine rpm increase with no load no shake...

I used the adapter from Mercedes 4x4 however I did not get the new yj flywheel balanced. Could this be my issue?

 

There is a typo for your adapter, can you clarify that? Did you locktite and correctly torque all your bolts and nuts in and on the clutch and adapter? Could be a bolt head. How bad does it shake, is it a visible shake or a vibration? Shakes are bad, very bad. I would say don't run it anymore until you find what ever is loose. Did you run it on a bench before you put it in the Jeep?
Speaking from experience it does not take long for damage to occur once you hear bad noises in the adapter area.
look for a loose bolt on your clutch assy I guess.
I did not balance my Mercedes Automatic conversion ( flexplate ), and it runs pretty smooth at speed, diesels are noisier than the gasser that came out

 

OK ya I figured it has to be something a bit loose or possibly its not sitting perfectly flush. I changed the typo sorry. Guess I'm going to have to do some work this weekend...

 

I must have pulled my mercedes In and out 4-5 times, before I finished. I still don't know your adapter. Do you mean mercedesdiesel4x4.com from PA?
Yes sounds like you have a engine pull in your future

 

Lol ya that's what I meant for the adapter sorry. I'm almost thinking it would be easier to drop the transmission. I will probably go by a dial guage today and check and variations on the flywheel and flex plate.

 

If you can I would pull the whole thing together,or In pieces, then try and test run it out of the jeep. Then you can dial indicator it on the ground , and stab it back in one piece.. For flywheel balance, I bought a cheapy Harbor freight balancer for the Kubota, I think it worked OK, but I did go to the metal shop and by a better center axle for it, you still need the dial indicator to check the axle on the balancer

 

Not sure about the vibrations but check your starter nose to flywheel clearance while its running.

 

OK here's what I did, I pulled the transmission last night before my wifes Christmas work party... Today I put the dial guage on different points on the flywheel while attached to the engine. I then hand turned the engine over using the power steering pulley so I could look through the engine bay and see the dial guage.

Surprise surprise it was went up on one half then down on the other.
Then I pulled the flywheel off and used the dial guage on the engine thrust bearing. Thank goodness there was no deflection.

After all this I pulled the adapter of the flywheel off the flywheel and noticed the bolts that held the adapter to the flywheel are a hair to long and are causing the flywheel to not sit completely flush against the engine flange.
Hope that makes sense.
I'm going to add a washer to each bolt so they don't seat to far in and push againts the flange...
I'll let you know if my theory is completly correct.
And thanks for your help!