Cocobolo has two things going against it. First it is extremely oily and might pose problems when gluing it. You will see/read all sorts of suggestions how to deal with this - some people suggest wiping with solvent (naphtha or DA) right before gluing, some say that will only bring glue to the surface. Some people suggest using epoxy rather than HHG or AR. The second problem is that many people have an allergic reaction to cocobolo dust. I recently built a coco bodied acoustic (the head is my avatar) and I made it a point to ALWAYS be wearing a dust mask when I sanded it. As far as scale length, that is one of the very first things that should be determined when you start thinking about your build. Again, Hiscock covers that very nicely. Scale length does affect playability (and probably tone but that is far harder to define). Longer scale has higher tension for the same strings (it goes up as the square of length) so it is harder to bend and slightly harder to fret. Obviously the reach between frets is slightly longer - most people can compensate. You need to move things around on your layout - bridge and pickups. You'll also find that most Gibson f/b's have 12 inch radius to match ToM bridges, Fenders tend to be 9 or 10 or even less (and of course most Fender bridges are not fixed radius). People do adapt Fender bodies to take shorter scale necks - Warmoth makes conversion screw on necks (the don't meet the body at 16) as well as some long scale bari necks. Again, it is much easier if you define that at the very start of your design and then make the geometry work with the scale. (Btw, I always like to select my bridge at the start and actually buy it so I can include accurate measurements in the design of the guitar).