Gasket Diameter - you would have to know what you have, just leave it as is as it will not change the compresion that much.
Deck Clearance - numbers are for stock, not decked. Again you would have to know what you milled off. Some are decking their blocks to zero.
Piston Type - stock is dished and the rest of the numbers are based on stock types. I went with flat tops fo I selected that option.
Note that all of the nuimbers that were inserted as a default are factory specs from what I have seen. Also, I went to at least 3 other sited to cross check the numbers and all came up with the same compression ratio. Some of them did not have all of the extra calculations such as dish relief, etc.
I will not have the engine running for several months as I am still deciding on exhaust and other stuff. I am taking this slow. I put in stainless valves and had a 3 angle job with teflon seals and 289 springs installed. Yella Terra roller rockers are going to be installed.