Engine swap, need help! >_<
 

I'm doing swap on my 01 elantra .I blew the head gasket on the old motor. I went out and bought another engine and its from a 2000 elantra with an automatic transmission . When putting it back together the transmission doesn't line up entirely. My elantra is a manual transmission, does this have anything to do with it not lining up? I'm new to the forum and just started doing my own little projects.