The recommended procedure is to lift the engine by 4-5 inches and slide the shaft below the engine. It is not too much work. Unbolt the engine, may be remove the exhaust hose if it is short then inflate a basket ball below the engine. Once you have enough clearance support the engine, take the ball out, slide the shaft out. A piece of cake. You will need to align the engine afterwards but you have to do this anyway if you are replacing the cutlass bearing.
You do not want to remove the flange from the shaft because it is factory aligned and it is unlikely you will align a flange on a new shaft as well. Actually, if you order a new shaft it will come with its own flange with instructions not to remove the shaft. The other benefit of this procedure is that you can do it in the water with minimal risk.