Some safes and computers will be locked again, so you can hack or re-hack them.
M1 - Confronting Sarif
M2 - Finding Isaias Sandoval
Taggart must be confronted with the evidence of Sandoval's involvement in the kidnappings, or have the evidence planted on his computer, in order for Sandoval to not attack Jensen and be suicidal instead.
If you fail to convince Taggart, you can no longer plant the evidence on his computer since you have already tried to expose his connection to it live on PICUS. As the Wiki walkthrough explains, there is slightly more XP to be had by hacking instead of confronting Taggart. However, by now you will probably have all the augments you need so XP no longer becomes critical.
Smash the State
To get four locations to search (each gives you 100 XP) you must have the Social Enhancer.
M3/M1 - Cashing in Old Favors
A Matter of Discretion, Corporate Warfare
The quest does not properly update after reading the pocket secretary but Zelazny is in the sewers accessed outside the Alice Garden Pods. They probably want you to look around for him instead of getting an automatic map marker for his location.
Fastest way of taking down Zelazny is with Takedowns. You can handle him and one other almost immediately with a Double Takedown. Eat Cyberboost bars if you have to in order to have energy to execute the additional Takedowns.
M1/M2 - Find Vasili Sevchenko's GPL Device
M2/M3 - You Scratch My Back, I'll Scratch Yours
M3/M4 - Stowing Away