Here is a link to a guy on Youtube who put a "tired" 440 in his. http://www.youtube.com/watch?v=7IljNkJjNnw
He said it would do 40mph but was still looking for a bigger motor. Trust me on this, 40 mph in an 11 foot boat is plenty. Mine does about 46 but will get you there before your mind tells your hand to back off the throttle.
I used the Seadoo, some have used Kawasaki, and Yamaha. It seems as if there is no best way - just your own preference. My preference was what I got a good deal on.
"I'm not trying to get it perfect. I'm trying to get it finished!"
Squirt Build: http://www.tubbytug.com/SquirtHome.html