Mine has a 12 x 9
My E29--and I believe most direct-drive Atomic 4 sailboats--has a two-blade 12 x 9 prop. This is over-propped and results in too little tip clearance. Better would be an 11 x 7 two-blade or one of the Indigo Atomic 4 replacement props which are 10 x 7 three-blade.
But Loren's right, what came with a direct-drive Atomic 4, correct or not, has little relevance to your Yanmar installation. I'd recommend a copy of Dave Gerr's book,
The Nature of Boats, which has a chapter on propellers. Gerr also has a very complete book,
The Propeller Handbook, which covers prop selection in great detail.
The Propeller Handbook is not for the math shy. :nerd:
You can also get recommendations from propeller manufacturers, Michigan Wheel for instance:
http://www.michiganwheel.com/MIWheel/propit/main.htm
CDI also has a listing by boat or by engine which would at least get you into the ballpark:
http://www.sailcdi.com/ppmain.htm
As you can see, CDI recommends a 12 x 7 replacement, but according to Gerr, a 12" prop has marginal tip clearance on the E29. Michigan Wheel recommended an 11 x 7 when I filled our their form and .......... waited.
Good luck.