In principle, the flange focal distance is the distance from the rear mounting surface of the lens's shutter, to the focal plane. The back focal distance is the distance from the rearmost part of the lens body to the focal plane. Neither of these distances is exactly to the center of the lens.
The extension required to focus a 90mm lens at 2 meters is found from the thin lens equation: 1/f = 1/d1 + 1/d2. Here f=9mm, d1=2000mm, so d2=94.2mm. So you need 4.2mm extension past infinity to focus at 2 meters. This isn't very much compared to the size of the camera, because wide angles don't take a lot of extension to focus.
Your best bet is likely to make a ground glass to put on the film rails and use that to set up the spacer and helical focuser. It's a good idea to leave some margin, in case the flange-focal distance is inaccurate - better to have a lens that focuses past infinity, than a lens that can't be focused to infinity.