Honestly, I'm not familiar with the mission itself, but I can give advice regarding player consequences:
Firstly though, how serious is your game?
- Gritty and tough?
- Slapstick and comedic?
1) If the players are wasting time (getting optical discs as collector's items, etc), then as GM, nudge them a few times with a pending deadline. In the mission, is there anything time critical? Can an informant be killed before they can talk to them?
-
GM:
Looks like you just missed a gun-fight. If you'd been here 5 minutes earlier, maybe you could have gotten the information the easy way...now you'll have to shell out some cred with your own contacts to find out what to do next...2) The Troll enforcers sounds like it was
hella' funny as well as being useful and positive in moving the mission forward

Only in-game consequences here should be some flowers from Nabo and maybe even an ongoing contact rating/romance.
3) Player with Penile enhancement trying to impress the guards? Sounds like a high-school prank which should end with a thorough beating... sounds perfect.
4, 5 and 6) Murder in a public area is bad. Sensors always pick up something, and just throwing a corpse onto a stage-show is going to give the PC's a bad rep. Breaking in and shooting someone in the stomach for interrogation techniques is on the same level..., and causing a riot at a stage show while info gathering is completely unprofessional
-
GM:
Your Johnson/Fixer calls, and they're furious. .. What the hell are you doing?! This job was supposed to be clean and discreet. Your pay is being cut by 1k each, and if I hear about any more idiocy, I'll cut my losses and bring in someone else... and maybe then send them out to tie up loose ends... are we clear?!- Also, someone may have seen the players, which means thast Knight Errant will pick up the security footage and start a file pieceing together the runners' activities (giving either
Bad Reputation, Hunted or
Wanted negative qualities, although these normally take
repeated acts of mayhem to start affecting the PC's