I think I hear what you are saying. If the geometry of the unit allows the bucket to curl up far enough and the dipper to swing back far enough, I could end up hitting the lift cylinder with the bucket if it is mounted underneath. Even if it isn't, large debris in the bucket could still hit it.
Since a hydraulic cylinder is stronger on the push than the pull:
If the cylinder is on top of the boom I will be able to push it down into things easier, but have less lift strength.
If the clylinder is under the boom, I will have less power when pushing down into things, but more lift strength.
I think I'd like more power digging than lifting, so I think I'll alter the plan to put the cylinder on the top. I can always switch it if I don't like it. It will change the total lift height or digging depth by a few inches, maybe a foot, but that is the fun of experimenting. /forums/images/graemlins/grin.gif
I saw that picture of the lawn tractor with FEL chained down lifting itself. Pretty neat. That whole website had lots of good pictures.