Most SC300's were auto also. The manuals were very rare......I am not sure if the trans. would swap between the 2 motors. Good question though, hopefully someone would have some insight on this. My take is that they would not be swappable.
Y not get a sc300 with a 1jzgte or 2jzgte already in it with a 5 speed. That way, you get the power you want and the manual trans. There are a couple being sold on 2jztrader.com right now you may want to check out.