The stage1 box is different, but AFAIK only in the bellhousing and transfer areas. The bellhousing for the V8 is different (but just bolts on the front of the gearbox so easy to swap). 
Perentie has the tapered roller intermediate shaft in the transfer and different high range ratio than stage1. Pretty straightforward to swap over the intermediate shaft and also need to swap the matching high range gear from the center diff.
The Stage1 output housings and handbrake are different from a 110/Perentie LT95. Stage1 has longer front housing, and rear housing has smaller handbrake (like rangie LT95's).
Pretty sure there are transfer selector linkage differences between the stage1 and Perentie but I don't have details.
Since its your main box thats got issues, if you can pick up another one with a good main box for relatively cheap I'd say grab it. You've then got the option of using it for parts to fix yours, or just swapping your transfer bits and bellhousing over and fitting it.
Steve
				
			 
			
		 
			
				
			
			
				1985 County - Isuzu 4bd1 with HX30W turbo, LT95, 255/85-16 KM2's
1988 120 with rust and potential
1999 300tdi 130 single cab - "stock as bro"
2003 D2a Td5 - the boss's daily drive
			
			
		 
	
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