1998 Dodge Truck Ethics

In May of 2007 I had extensive work done on a 5.9l Diesel Turbo 12 Valve engine.

Reseal Vacuum Pump
Install Boost, pyrometer and Trans Temp gauges
Installed Fuel Plate
Installed Fuel Injectors
Cool air Induction
Replace Torq Converter, Valve Body, DD Trans Pan
Installed Extra Deep Trans Pan
Replaced Turbo
Extra Exhaust Pipes.
Cost $5,500.00

Today, after taking it back to them with a noise 'down low in the engine' I am being told the Main bearings are out and the entire lower engine needs to be replaced. Cost Estimate: $7000+

My question is this: When all the the work in May, should they have known, checked, heard or looked to even see if the engine was in good working order before doing all the upgrades and repairs?