I thought this would be helpful, and clear up what year transmission would be best for this swap. Dave just posted this on his FAQ on MazdaTrix's website.

I am in the middle of this swap and almost wasted time on the wrong transmission.


Need 1994-1997 1.8L Miata
( https://www.mazdatrix.com/miata-1800...sion-pictures/ )

 

Thanks for posting this info, I built one of these this winter using a 1989 Miata transmission as a donor, and I saw this misalignment as well.
I checked to make sure I had it together correctly, and couldn't find a problem so I bolted it all back together and it works great.
I think since it is on 4th gear it shouldn't cause a problem, there is less torque multiplication.
I did the project mostly for the better ratios, so I don't mind having the one piece synchro.

 

the miata trans is the same internally from 1994-2015