John-
It's measured from the transom to were the engine mount touches the bracket mounting area in a strait line. I wish there was an easy way to answer the second question but alot depends on the construction of the bracket. All references made to mounting height of the engine are in relation to the anticavitation plate and it's height above the keel.
I were brave enough to take on a big project such as building my own bracket I'd base everything on were the anticavitation plate needs to be at 30 inches behind the boat. Make a mark at 2.5 inches above the bottom of the keel and design the bracket around that. I'd go with smaller tabs so you can build as big a flotation chamber as possible.
Some reading material:
http://continuouswave.com/whaler/ref...eBrackets.html
http://www.stainlessmarine.com/insta...ketsingle.html
http://www.stainlessmarine.com/bracketlayoutsingle.html
Strick