Yamaha Lowerunit compatibility help?

I have a good running 2 stroke 1999 Yamaha 40hp OB that the lower has went out in.
I have just been told by a guy at the yamaha shop that all 2S 40-50hp lower units are compatable with each other as long as they are 2S. I have found several Complete OBs and good lowers for cheap, but I have been told by a few that some models will not work on my 99 due to changes throughout the years. Now I am confused. If any yr model will work than I'm in good shape because I know where a cheap one is sitting. If not I will have to continue my search...
Any help or insight on this topic would be very helpful.

If you don't get a answer on here try on Iboats.

A lot of the 2 stroke 40 and 50 hp motors were interchangeable, yes. But not all of them. There were a few minor differences...minor enough that just picking up another foot of an unknown motor could possibly cause some issue. Also long and short shaft can be a problem too.

What is your motor model and serial number? I may be able to get an interchange listing....