Usually when you purchase an engine swap everything (ie. new mounts, harness,ecu,tranny,shift linkage, axles, etc....) comes with it.

I'm not sure about what is all needed to convert the auto to a manual os I will leave that to some more experienced people on da board.

B16A-----> JDM (168hp @ 7800 rpm and 116 lb/ft @ 7300)

B16A2---> USDM 99-00 (160hp @ 7600 rpm and 111 lb/ft @ 7000)

Hope this helps a little