hello there.
 Theres only one real issue besides the missing parts . The valve body is setup for a engine that has allot more torque than the little 2.0 .The shift points will be wrong and it will not run correctly. However it wont hurt anything. Just wont be like it should.
 
 You will need the c4 bellhousing for a 2.0 as well as a specific covertor and a flexplate. After that you need the correct rubber mount to mount to the transmission crossmember. Also don't forget the starter,and the downshift linkage that works off of the carb and the downshift  link that connects to the trans.
I wish i could tell you where to get this stuff as junkyards have just about run out of pintos in allot of areas . Ebay sometimes has stuff. never know who might have stuff here as well.

 I have the little link that connects to the trans, I THINK i have the downshift "bar" that goes from the carb to the trans,and i have the Pinto c4 valve body that has a B&M kit in it .It shifts pretty hard. I'm using a V8 valve body in my conversion now so i wont need the old pinto 4banger body.
 After all is said and done might be easier to rebuild the 4speed ?? Just a thought.
 Hope this helps!
Robert