I think the dealer quoted you $900 to replace crankshaft bearings and have 1 tappet reground, because they assumed the broken bearing was the CAUSE of the oil pressure drop, instead of a RESULT.
When they found that the broken bearing was the RESULT of the broken bearing, and not the CAUSE, (because the engine pumped all oil out as stated in the bill, "tractor came in with no oil in it") they probably found that your engine was a total write off because all other moving parts (camshaft, cylinder walls) have ran dry as well.
Because these Ford engines are so called "parent bore", which means that the cylinder liners cannot be replaced, it is usual that the engine is thrown away and a new engine, or shortblock, is installed..
I think the oil pump was replaced because it failed, this causing the oil pressure drop ?
I disagree about it being necessary to replace the turbo when bearing shrapnel has been in the oil: engine lubrication oil pumps normally always have a suction filter to prevent that it goes into the lubrication system.
However, because your engine starved of oil (dealer found NO oil in the engine when it came in) i'm pretty sure the turbo was dead too...
To sum this up shortly, i think the dealer assumed that 1 crank bearing broke, causing the oil pressure drop.
When they opened her up, they found that the bearing was a RESULT of the oil pressure drop, not the CAUSE. That means that there was a high chance that all other bearings were damaged too, as well as the camshaft bearings and the cylinder liners. In that case agree with their decision to not put any money in the toasted engine.
However, as you say, afterwards it would be cheaper to get a complete new engine, because of the workshop labor hours savings.
I dont think they replaced more than they needed to, because they even went with the shortblock instead of a complete engine, but they lacked in informing you that the problem was far worse than they expected and that the engine was a total write off....
I agree that they should be able to show you the old parts: I once had a transmission of my car rebuilt at a tranny specialist: They sent me all bearings they had taken out, with it in the box, as proof that they didnt just charge me 913 Euro for pressure washing and painting her up nicely.