I very recently did that exact thinig. I had put an M41 in my PV in place of the nice M40, only to find the M41 had some non-operating syncros (#'s 1 and 3).

Initially when I tooke them both apart I mixed and matched and came up with the best looking set of gears and bearings. Then I noticed the layshafst were different diameters, so I had to use the slightly more worn looking M41 layshaft. Then, upon reassembly I found I couldn't quite get the layshaft to drop down into position - it just wouldn't go that last 20th of an inch. After about 15 tries I finally took everything back apart and noticed there were slight differences in the gear diameters between the two sets.

In the end the ONLY parts I was able to use from the M40 were the syncro cones (I verified that they had the same part numbers). Everything else was different and couldn't be swapped. I could have either used the M41 case and all the M41 guts or the m40 case and all the M40 guts (AFAIK the output shafts were swappable too) but the fill plug on the side of the M40 case is an inch or so lower than on the M41 case - although that isn't really much of an issue as I generally fill mine via the shifter hole anyhow.

Alls well that ends well, onse using all the M41 gears and the M40 syncros it went together easily, back in the car it now has syncros on all 4 gears and doesn't make any funny noises.

NOTE - I don't necessarily think the difference between my 2 trannies were the result of them being an M41 and an M40 - rather more the difference in years of manufacture. I'm not sure of the year of the M41, but with a J-type OD it is certainly newer than the original M40 out of my '63 PV.