Without being able to see all the details from the pix of the new one (the old one is mostly scrap) it looks as if the input and output members aren't correctly assembled, and the position of the gear looks too 'low' as you say.
I think it needs taking apart for checking that the components are in fact the correct ones, and are all there, and that they are assembled in the right order.
Correctly assembled, the tabs on the two parts of the unit (which limit the movement) will close to almost 100% of their depth, not like that one, where there's only partial engagement it seems. Could that be due to the thickness of the linkage parts the springs connect to - can't see enough to be sure, but they look a bit chunky from here? Or is something not seating properly on one of the pins maybe?
For a picture of typical unit, see
http://www.brightsparkmagnetos.com/faqs/FAQs%20about%20ATDs/How%20does%20an%20ATD%20work.htm, or the very useful "ATD Repair" document on the site of Priory Magnetos:
https://sites.google.com/site/priorymagnetos/atd-units - and follow the link in red type.