Thrust bearing ?
 

My Atomic 4 is a direct drive engine. When I switch it to forward it makes a strong grinding noice. In neutral or reverse it does not. Could this be a defective thrust bearing? Is there a way to tell if the bearing is deffective?

Well, the sure fire way to tell is to replace the bearing. If the noise goes away, you know the old one is bad.
Other than the bearing, well... Any chance you dropped something in the transmission case that's rubbing on the outside of the cluster? The cluster rotates in forward, but not in neutral or reverse. Do you see any rub marks on the outside of the cluster?
If it only grinds while shifting but not when in forward, it's probably the bearing on the shifter.

The first thing I would do, if you dont have a reduction gear.
Try crabbing the shaft coulping and try moving it back & forth to see if there is any play in the shaft/ thrust bearing . You should'nt have any.
Also check for oil around the retaining flang oil seal
I dont know if this test would work with a reduction gear assembly .
Cheers Rick

Another thing to check is the pilot bearing. Remove the gearbox cover and try wiggling the drum.

Have you tried the adjustment procedure?