I was talking to birdman about this off-forum and either it's an exhaust issue from being unable to torque my manifold bolts to spec or something else has gone wrong since the engine was rebuilt 8 months ago. Yes it had a very carefully monitored break-in period.
You start the car cold and it cranks fine, starts fine and revs fine. Give it about 30 seconds and it starts making a clicking or clacking like you expect of a diesel engine. Becomes more pronounced with load and it changes with RPM. Sounds like piston slap, but this has bored cylinders, new pistons and new rings. Bearings are unlikely as that is all still basically new as well. I doubt the rings have failed to seat.
But the weird part is you give it two or three minutes and it goes away and doesn't come back again under load or RPM until you park the car and let it go cold again.
Talked to the machine shop because it's still under warranty for another four months and they suspected it is a very small exhaust leak that opens as the manifold warms up but seals again once its hot. They are aware that the manifold has been machined because I brought it into them last November because I found it had a bad warp and a burned gasket.