Looking at a late model Fountain 38L, 525s, ITS drives with stubbies. Obvioulsy this set up is for mainly top end. When
you compare this setup to a more conventional XR drive setup
what are the handling diffs? I asssume the more conventional
XR may have a better hole shot and handling from low to mid
range and better low speed maneuvering. What should I
expect out of the ITS with Stubbies, just a better top end,
what will I sacrfice?

essentially there is no sacrifice. maybe a second during planing.literally. i have set up and dialed in quite a few of these exact setups.
there are no handling issues even at low speeds. the sportmaster lowers have an extra large skeg to offset any handling issues that might occur by using stubbies. imcos lower is slightly less, but still handles very well.
the its sets the drive back further into harder water which offsets the effetcs of the lowers.
the efficiency of the fountain bottom is simply incredible. the typical offsets experienced by some other manufactures hulls just dont happen with the beaks. not to say they cant, but for the most part i would not worry.

stubbies??????

I'm assuming you mean shorty lowers. How short???-1, -2 or -3 inches. Pretty common to go from standard length and 4 blades to -2's and 5 blades.