I cannot see how the diff problem could have anything to do with the clutch.
As you seem to have concluded, it is box (or engine) out time. The actual problem will become apparent when it is out. 
As I see it, there are several possibilities - 
1. Clutch fork is damaged (common)
2. Release bearing or its sleeve is damaged (uncommon)
3. Clutch driven plate is warped or broken (rare)
4. Pressure plate is damaged (never seen one, but could happen)
5. Spigot bearing is dry and dragging or seized (not uncommon but usually very noisy for a long time before any other symptoms - may make parting the engine and box difficult)
John
				
			 
			
		 
			
				
			
			
				John
JDNSW
1986 110 County 3.9 diesel
1970 2a 109 2.25 petrol
			
			
		 
	
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