I know this isn’t the right way to solve my issue but I have a 98 civic lx and I’m not a fan of how it’s shifting, so I sourced a cheap 98 civic ex transmission ( just because my transmission is scarce where I live) so what all do I need to do when I rebuild this trans to get it functioning properly in my ride, both are automatics

 

You failed to mention if it's automatic or manual.

 

I corrected it but automatics

 

If I remember correctly, the 6th gen 96-00 had more electronic controls to the automatic transmissions so you can't use a different trim's automatic transmission. I believe it throws the car into limp mode if you do.

It's unfortunate that transmissions are scarce in your area as you will need another 96-98 LX automatic transmission to swap in while you attempt a rebuild of your current LX transmission.