What are the major differences in operation of these motors? I am thinking of getting a mud motor.
Every one has told me to get a surface drive. Pretty much stay away from a long tail.
Thoughts?

A long tail has its place. But unless you need the long tail, the surface drive will probably handle 99% of what you need it for

Ok but where would the long tail be a improvement over the surface drive?

Serious stump fields, and constantly climbing over submerged logs etc. If you have room to get on step, surface drive all the way