Is this a total strip down and rebuild?  If it is just a re-seal then: 
 
Take the top trim off.  Clean the glass throughly via razor blade.  Get any loose silicone off.  Very time consuming. 
 
Corners - use masking tape 1/2 inch or so away in the corners and a plastic spoon to smooth out the silicone.  Remove the tape immediately after so the tape and silicone does not dry together. 
 
I used GE Type 1 silicone and have had no discoloring (1 year later now) 
		
	
		
		
		
		
		
	
		
		
	
	
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