First off, the bolt pattern is 5 on 5 1/2", not 5 on 5. That is what the stock front axle is btw. As far as gears with a flathead, I would defer to those with experience with the engine (not me).
Mine came with one already in, but I had to pull it and re-mount the perches as the pinion angle was around 12 degrees. You will also need the driveshaft yoke to fit the 9" to get it grafted to your driveshaft.