Yep - the output shafts are not the same. The M40 has a stubby little one, the M41 is about 6 or 6 inches longer. To swap output shafts you have to have both a donor M41 (to get the shaft) and take the M40 apart about as far as it will go (I guess you could leave the layshaft in). It's not like many OD units that just use an adapter and slip onto a regular trans. The only way that would be worth it was if you have a completely hand-grenaded M41 with a good OD unit on it, you could probably get it to work. Note that over the years (not necessarily an M40/M41 thing) various internal parts changed - bearings, gears, etc Not all parts from all M40/41 transmissions will interchange.

Just get an M41. They go by on eBay occasionally. Don't worry if it is an 1800/late model 140 unit with the remote 'short' shifter - you can unbolt the 'long' shifter top from your M40 and use it on the M41 (after you drill and tap the 4th gear switch). Then, depending on your luck, some potential fun with differing flange sizes. Your driveshaft will need to be shorted approximately 11 1/2 inches (you should measure this yourself several ways - not everyone seems to come up with the same numbers, luckily it isn't an incredibly precise thing - the driveshaft as a telescoping spline between the trans and rear axle. Shortening the driveshaft is a precision thing - it has to be straight and balanced afterwards. I took mine to a local drivetrain shop that build custom driveshafts. They shortened mine for $50. An alternative is to get the driveshaft from the donor vehicle if possible, or at least the front section.
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I'm JohnMc, and I approved this message.