I just posted to your other thread. I had to pull my 406 due to thrust failure. I had a cast scat 9000 crank. I now have a forged crank going into my engine. The forged crank was trued and re-heat treated, so it is now 10/10. The new bearings will be "H" bearings vs. the cheaper "p" bearings that the last builder used. The H bearings are supposed to be a better material and have the proper radius for an aftermarket crank.
My engine builder has all his cranks checked, even when new, for proper tolerances. That is the only step he has done outside of his shop. He said that even some new forged cranks have inconsistent heat treating, which is evident when he drills the crank for balancing. He checks the rods himself, before installing.
It seems that many manufacturers have quality control issues now days.
People tried to tell me that my trans caused the thrust bearing to go out. It is possible, but my uncle owns a trans shop and does any work I don't do. He checks for those issues and also use an anti balloon converter on my trans. The engine guy is best friends with my uncles right hand employee, so his word is as good as any trusted person. He has seen quite a few crank issues from bad machining to bad heat treating to the wrong bearings used, and some transmissions that were setup wrong. His crank guy said he has seen many cast scat cranks with issues right from the factory as well as many other brands.
My trans was built with many upgrades and was set to shift hard (my request, but most from my uncles shop are set for a firm shift.). It is possible that my trans put an acceptable but high end of the scale amount of force and the crank and combined with the wrong bearings and a soft crank, it may have created the perfect storm. My trans was toast. The crank movement sheared some teeth where the TC and trans pump meet, which sent metal through the trans and killed it, wiping out the case and drum in the process.
The engine and trans were pretty messed up and it was hard to tell where the problems started and where they ended. Now, we are trying to address any possible points of future failure.
OP, you guys made the right call to pull the engine. Just make sure that you have the crank checked for proper geometry and you use the right bearings, then make sure the trans has the proper clearance from the crank.