Other than the ports in the main webs and the cam size, what are differences between the ls6 and the ls1 short blocks?

 

The improved LS6 oil pump is one.

 

http://www.idavette.net/hib/ls6/page2.htm

 

will ls1 cylinder heads using stock head gasket net 10.1 compression? Are the pistons and compression height the same as an ls1? (could not find that using the search button)

 

if your refering to using ls1 heads on an ls6 block then yes with a stock gasket you'll be at 10.1 compression. the ls6 gets 10.5 by using a 64cc chamber.

 

The GTO is advertised at 10.1:1 with the LS6 block and LS1 heads - FWIW.

Edit - when I originally posted this I misread the terminology and thought you were saying 10:1 - just so I don't sound like a complete maroon repeating what's already been said.
Dan