A summary of the three papers is here: http://media.utoronto.ca/media-releases/traffic-emissions-ma... They just set up some measurement tools by the side of the road and waited for cars to drive by. They didn't check the "tune" of each car or test whether any kind of tune-up would change anything.
Edit: more links!
Naomi Zimmerman's webpage: http://naomizimmerman.com/publications/
Abstract of the relevant paper: http://atmos-meas-tech-discuss.net/8/2881/2015/amtd-8-2881-2...
This PDF is labelled "supplemental" but it looks like the full text of the paper. http://atmos-meas-tech-discuss.net/8/2881/2015/amtd-8-2881-2...