Question about Long or Short shaft for Inflatable.

I've read so much today about how inflatables should always use a short shaft.
But the electric trolling motor specifically made for this boat is 36 inches.
And after using it a few times in the CT river and once in Stonington...I learned I really had to drop the shaft as much as possible because of chop or wake.

I'm interested in purchasing a Yamaha 2.5 4 stroke or a Honda 2.0 HP 4 stroke or the like....but I've seen some videos on youtube where people with my boat (Intex Mariner 4) hit the throttle a little and the stern goes way up in the air...

If I measure the top of the transom to the bottom of the keel it is 19 inches.

Boat:

http://rubberboats.com/product/inflatable-mariner-4-rigid-inflatable-boat.html

Current trolling motor:

http://rubberboats.com/product/intex-trolling-motor.html

Current motor mount:

http://rubberboats.com/product/motor-mount-kit.html

I'm not sure if I explained clearly but when it comes to choppy water in that boat, its easy for the prop to come out and when it does, especially if there is a stong current, its difficult to get going again.

Intex says its rated up to 3 or 4 HP but does not state the length of the shaft.

an example of boat being pulled under in the back.

http://www.youtube.com/watch?v=z4FCtmZA5Tw

This seems a better example of how im looking for a motor to work with the boat:
http://www.youtube.com/watch?v=y-DSEKrUZg0