The StewMac plans that I used for my 000 are long Martin scale. Short Martin scale is 0.50 inches shorter, that means the bridge shifts towards the neck by a quarter of an inch. If I was building a short scale guitar I would move the X, bridge and first tone bar 0.25 and the second tone bar maybe 0.125. You just have to pick something and go for it.
Some of the vintage Martins did not have popsicle braces, when I had my '74 D-18 hot rodded I decided to not have it removed. I put them in every guitar that I build. My understanding of top movement says the upper bout have very little contribution to the sound, I would rather avoid failure. As Clay says, pick yours
This was my first guitar - it is 12 years old now and still my favorite. I didn't know poop when I built it, must have been blind stupid luck