You've run into one of the more common problems encountered in making this swap. There are two types of flanges, 3 1/8th and 3 3/8th, and rarely do you get lucky enough to have the same size on the tranny as on the shaft. There really isn't a better way to go: you can try to find a matching flange for the M41 or for the shaft -- depends on what's more available in your neighborhood. I've never tried to change the flange on the shaft, but it might be the simpler way to go since you have to have the shaft cut for shortening anyway. Finding the right replacement flange for the OD unit can get tricky because M41s come with different numbers of splines on their output shafts. I haven't found the rhyme or the reason for this, but I'm sure there is --maybe someone will jump in to explain it all to you (and me). (Friend of mine has been looking for a 3 1/8th flange to fit an eight spline shaft for months) At any rate, if you decide to change the flange on your M41, hold on to the old one. Someone is bound to come along in desparate need of it. BTW, if it's the larger type of flange you'd be putting onto the shaft, make sure it fits through the shaft bearing carrier. Since yours is a 67, it probably would, but you're better of sure than sorry. I'm sure you are aware that a flange coming from an M40 won't fit on an M41.
Bob S.