i just got a a si tranny from a junkyard and when i went to put it in my car it wouldnt line up so counted the teeth it had 21 so i was wondering what is the main shaft from if its not d series

 

88 Si has a 21 spline count on the clutch spline
89-91 Si has 20 splines
This could be where your problem lies

You will need a clutch for the 88 Si transmission

 

that so weird, i believe you even the lining tool from a y7 lines up to my clutch

 

Yup, you sir have the 88 Si transmission

 

This thread below touches a little bit on the differences
It may be helpful to you...

https://honda-tech.com/forums/honda-crx-ef-civic-1988-1991-3/what-look-identify-si-tranny-1551508/

 

its that 1 and only year in all the 88-00 that have different teeth

 

Yeah its odd, but that's the way it is I guess
Here is another thread as well that could give you some insight on what to use to make your transmission work for your setup.

https://honda-tech.com/forums/honda-crx-ef-civic-1988-1991-3/stock-clutch-fitment-guide-2284956/

I hope all of this helps for you......

 

thanks for the help much apreciated