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			From your pictures the shaft was cut like you said. 
 
Then I see a picture of the mushroom shift knob used on a 1997-1999 2.5.  That knob will no longer lock down because the groove has been cut off.  And the boot has been cut off the knob. 
 
Then I see an aftermarket shift knob that would usually screw into a threaded round shift lever, but the Box has a flat lever.
		 
		
		
		
		
		
		
		
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