D16 bent crank?

Honestly how can they tell the crank is bent by looking at it.
I would bring it to another shop and check the bottom end bearings. Sounds like a bearing issue . Excess bearing tolerances will give you your symptoms.
As to why?? Good question. Could be a bunch different reasons. I would just pray that no harm is done to rod@crank journals yet and if all good roll a set bearings in and go trucking.

But a bent crank, highly unlikely.

 

Roll bearings in ASAP

 

Can they show you where the problem is? Would a rod not knock? Maybe a main or some thing else? Thank I would have it towed and built or maybe a salvage engine.

 

Unless they're magicians, I don't understand how you could possibly check a crank while in the block.
54K sounds way out of bounds

 

Bearings...but hopefully not from THAT shop. They should be able to show you samples from the rod & main brg caps and will show the bearing wear

 

A crankshaft is precision balanced. If it were bent one would think you would feel a vibration or something. Only way I could see checking to see if it is bent while in the truck would be to remove all the caps except the front and rear, then check the runout with a dial indicator at the middle main journal.