Depending on the brand, I would say 10" for the skegs. More importantly is where does the propeller line up in relation to the rear cross-member.
Mine is a Hydrolift and we had to extend the space between the cross-member and the prop as it lined up directly on top of it.
"Untreated wood" Why? / You are covering it with carpeting or something to protect the boat right? / That means it will stay wet for extended periods. You need the pressure treated stuff.