The last time I rebuilt and M41, I do recall that getting the nut off that holds the flange to the rear of the output shaft was a bitch. I may have used a large pipe wrench on the outside of the flange, because I still have that larger flange and it's got bite marks in it. You could make up some spanner that bolts to the flange through some of the 4 bolt holes that join the flanges. I don't know if putting it in gear would lock it up enough to remove the nut without damaging the gears. For sure I'd remove and replace the rear seal, and make sure that the replacement flange you get has a good sealing surface. Those rear seals are a likely point for oil leaks with a worn flange sealing surface.