Here are the two spots to find Johnny on the can:
1. Once you find Ames (Shell 1 Core, Level B1), he will tell you to listen in on Ocelot and Solidus's discussion. Instead, move the mic to the left - there is a bathroom in the corner (apparently)
. Listen until he stops talking (and crapping) then go back to the original objective.
2. After you find Emma, and you get her safely to the walkway below Strut L, you will see 2 other Struts that Emma will be walking towards. You will need to defend Emma from enemies (soldiers and flying turrets) with your sniper. Once Emma gets to the second strut, pull out the directional mic -
Trophy should pop after the second discussion.
Questions, corrections and neg vote justifications below.