It might be ok depending on how long it was ran. Nytro/Viper motors run very tight rod/main bearing clearances, usually .001" to .0015" and the first thing to show oil starvation damage will be the rod bearings.
When you have the oil pan off I would go ahead and pull the rod bearing caps off and inspect the bearings/crank. Normally the PTO and center are the first to show damage.
If the rod bearings are not scored and the clearance is ok, then very likely the main bearings are ok as they receive oil before the rods. If the rod bearings are scored then you'll need the separate the crankcase halves and inspect the mains as well.
The bottom end is rebuildable and crankshafts/bearings are available from Yamaha.
Normally the cylinder head will be ok with the following exception.
When you inspect it and find that it has a spun rod bearing. Then you'll want to pull head and valves to check them for straightness. What can happen when a rod bearing spins is that the excessive clearance allows the piston to travel farther up the bore. When this happens the piston can contact the valves and bend them slightly. If this is not caught during the rebuild the bent valve stem may cause the valve to "hang open" and contact the piston bending it even more. Once this process starts it's only matter of time before the head of the valve breaks off and it's game over for your engine.
The main thing is to check the bottom end BEFORE you try and run it. If there is rod bearing damage and you try and run it, there is real risk of spinning a rod bearing and pitching a rod through the side of the block.
Nytro/Viper engines are very durable and usually will last a long time, however one thing that can kill them is oil starvation.
Bill