hey guys i hope you guys can help me out here please

im doing a swap into my civic si 2003 i currently have a k20a2 and im taking that out and adding a k20a is suppose to be a jdm motor. point is that im also upgrading my clutch to stage 2 but for some reason my transmission from my old k20a2 wont fit into my k20a. someone please help and tell me what i need to do?