Well, 1.25 is a good deck height, I'd use that. Again, you will not get exactly the same readings around the piston because of the piston rock as a result of the piston/wall clearance. Set your piston dome even with the cyl. top like you did with the straight edge and then measure down to the lip with the caliper and compare that to the .525" that JE says the dome height is.

Hijack
 

My burette finally arrived.
In my case, my 9.5 JE pistons, spec'ed out as specified.
Deck height at 1mm with .25 base gaskets.
http://forums.pelicanparts.com/uploa...1465528717.jpg
Here I'm confirming the dome height, .400" or 1.016cm
http://forums.pelicanparts.com/uploa...1465528830.jpg
Here I'm verifying the dome volume. 39.4ml. Spec is 39.8.
http://forums.pelicanparts.com/uploa...1465528923.jpg
With my heads measuring 89ml my CR comes in at 9.8 to 1. Right where I want to be.
BTW, I used Excel to do my calcs. Makes it easier to fiddle with the numbers.

Forgot to post the spec sheet.
http://forums.pelicanparts.com/uploa...1465529306.jpg