MakerBot Print is our newest print-prepration software, which supports native CAD files and STL assemblies,
allows you to interact with all your printers via the Cloud, and many other exciting new features.
Point 1, is correct. Print area is between the heads of the screws so you have nice flat surface. You can extend it slightly if you want more space but than at the corners be aware the countersunk screw heads have to be a bit under the surface so you won't damage the nozzle and printed filament is not going to stick to them. Than you may have almost 116x116mm big print area.
2, Yes you will have to recalculate (calibrate) the steps per mm to get correct values for your machine. The real size of printed pulleys, belt tension and real gear ratio of your motors is influencing the values a lot. Initial numbers are there only to get thing moving.
For Z axis it is best to print some tall calibration cube of known height, measure it and recalculate the steps per mm accordingly. You can also follow my reply to Eddiiie: http://www.thingiverse.com/thing:945156/#comment-1191875 where is the calibration of movement explained in detail (you will have to copy the link as it won't open correctly)
I am not aware of safe homing behaviour as I am mostly using Marlin 1.0.0 and 1.02 where it is not implemented yet. I think you can keep it if works correctly for you.