I had looked into this conversion quite a bit, before I decided to do a period correct build on my pinto.
The Type-E 4 speed on your 2.0 will bolt onto the zetec, although it will require a little bit of modification to block the opening created. I believe the original Pinto starter can be used, but will need to be verified as I cannot remember.
The largest hindrance to the zetec on our platform is the cross member and steering rack. You can either go dry sump (dont even have to worry about it then), or pick up the pan from RWD motorsports.
There is plenty of room in the engine bay with it in there, and the opposite intake and exhaust is not an issue (get a short header).