Well sure, I'm happy to talk about it. Spoilers abound guys.
When you ask about pitfall, you mean those made by system conversion (or lack of it) as well as the unforseen actions and reactions of the players to the plot, right?
Well for the first, the major pitfall might be NPC stats. For instance, the skills and attributes of most NPCs in that story are too high. Not all mind you, a charisma 6 Euphoria fits perfectly, but all the mages have magic 6, while your PCs probably doesen't unless they're very experienced.
Still, even though I didn't really reduce stats the team had no difficulty taking down the Knight Errant sec in Pacific Towers. So I advice not to reduce all stats across the board, just the Mages (possibly) and if you feel they are too high for average grunts (I don't see KE as average though).
What you probably want to change is to give most NPCs comlinks of fitting type (Euphoria should have a really expensive jewelry type, but since there are no NPC deckers in the story they should't have more than a basic Browse and Edit.
Now, for the Pacific Towers computer system. In the story they have a security terminal in the lobby. Now you're free to give them wireless, but what I did was just to let the luxury apartments have outdated technology... after all there are probably hotels today with 20 year old telephones in them, or maybe fire alarms and stuff like that.
That meant the team actually needed to get into the lobby, deal with the security guard and valet, and jack in old style. I'm sure commlinks still have that function to use on old terminals and go in VR, but I let the terminal have a tridscreen as well instead of AR. Now the system in the module is described as Orange-3 or some such (gibberish to me), but I assumed that it was not very secure so I assigned it mostly rating 4 firewall and programs, and a single IC of the same kind and a Data Bomb. Despite this Jimmy had only rating 3 programs at this time and didn't even have defuse, so he had to spend alot of edge just to get through. If your hacker is tough one with rating 6 programs and high skill you might want to up the challenge a notch (but not too much).
As for the Maglocks I just used the existing ones at the same ratings, but because of the lobby guard you can't start hardwaring them without detection.
If the team thinks to enter via the glass veranda, you need ratings for the glass - I just used ballistic glass though since SR1 barrier ratings aren't known to me.
Oh, and my players suprised me with wanting to rent an apartment in Pacific Towers to stake it out, and there's no price for them in the module, so you might want to think ahead and make one, or just say it's full. I can't remember the price I assigned a "cheap" one in there, but it did cost pretty much and could only be rented for 1 week or longer stays. Since the apartments (except Euphoria's) are at least High Lifestyle, I suggest at least 2500 per week. It should be enough to make the players balk at paying so much compared to their pay. Not that it did with my players

Hmm, oh and the magical security there was pretty tough. A magic 6 magician, an ex-shadopwrunner, and two force 5 spirits (one guarding miss E against spells (don't think they can do that in 4th ed but I let it still). An astral wandering mage is likely to get into combat with these two, so that can be challenging.. and if the mage wakes up they're in serious trouble.
Map. E's has a bedroom, but the only way there according to the condo map is through the "jungle" room, a bathroom and an excercise room! Also there are no locks inside the building which makes it very easy for teams already in to move around. However in the game both me and the players though it ridiculous that E had to walk through all those rooms to get to the living room, so I made a new door directly from her bedroom to the living room. The time I played with a different group the team got in through the jungle glass veranda using explosives and a silence spell, and then simply made a barrier on the door to the living room and picked up E at their leisure while the guards could do nothing.... an extra door prevents this at least.
Another pitfall is when the team has taken E, and waits for the payment. Now, the runners might well choose a different location than the one provided by Mr. J, but the module foresees this and pretty much tells you no problem. But my resourceful team as you know took her to an underground lair and shut the blast doors! Which meant the team had an insane tactical advantage as Shaka and his goons had to go through several doors in order to reach the runners, giving them time to line up with assault rifles and grenade launchers to make mincemeat of them in the first initative pass.
You may want to increase the number of guards, or improve their weapons and armor. Heck, you may even give poor Shaka an armored jacket or at least a powerful Armor spell on him to give him some chance (but tribal leathers are much cooler). The only reason why Shaka proved a somewhat memora ble foe was because he did his style 100% (foolishly brave, agressive and direct) and because he went astral and manifested before the PCs to scare them. But it is important that you give Shaka a very high Ritual Spellcasting skill and allows him to use the material link rules in Street Magic, and let him track E down with it (even through a force 4 ward). Of course, if the PCs make enough precautions they might just avoid the encounter altogether, but Shaka is supposed to be very good at finding people.
Another pitfall in the hostage situation is E herself. Ruthless PCs might just decide to drug E all the time, to avoid her recognizing them. That happened the first time I ran it. BOORING. So encourage the team to let her stay awake (and interact with her, as that's fun) by having sedatives be dangerous to overuse. Basically when the team started injecting her with too much Narcoject she began to take physical damage and Simon with his medical skill could tell them she couldn't take more drugs. Besides, stress the fact that she's an international Sim Star, and that most of the runners probably would PAY to be in the same room with her. If you had access to your favourite female singer/actress, wouldn't you at least want to talk to her? (and if bad PCs wants to rape her, remind them the Johnson said she was to remain unharmed and treated like a queen - professionalism if not morals should stop them (or they screw up and don't get paid).
The worst thing that can happen is if the team somehow lets Euphoria die - in which case the adventure is over except for Mr. Barrones teams going in to extract vengeance.
BTW a question the players raised deserve to be mentioned: If E's manager wanted E back so badly he hired a mage to hunt her down, why didn't Es bodyguard and protection mage join in the hunt as well? Well I said it was because they were fired for incompetence (yet the players thought they were powerful because of the force 5 spirits), but really I don't think it makes sense either. If they do join, the team needs a tactical advantage (like mine had) in order to survive, or the mages needs to have much lower magic (4 and 5 perhaps), but you could remove the goons then. Or make a better excuse for why the bodyguards didn't get a chance to bring E back before getting the sack.
Well, after E is delivered and the team is paid, the group felt pretty good about themselves... that was to change. The way the module handles the recruitment of the PCs for part to is very bad - obvious railroading. The module assumes the PCs identities are all known to the Mr. J that hired them and the Fixer Ellory Whitecastle (which might be a stranger as well, or should not be a PCs permanent contact because he automatically loses it.
Then it assumes that the PCs can all be tracked down very quickly and forced to meet with the ones the PCs just worked AGAINST. Yeah, cool plot twist, but at least 1 player felt really screwed by it, and even mr paranoid got caught a tad too easily. So my advice here is to allow the more careful or paranoid PCs to avoid capture, and just have Barrone talk to the ones that can easily be found. If all the party are like the former, then you need to have them be setup or lured into a trap... or basically say "Congratulations you managed to evade the last part of the adventure. Have fun living under a rock!"
Now playing out the actual briefing by Barrone is fun (and I used a voice similar to the Walton Simons in Deus EX (not the rich one, his lieutenant)). A similar sinister voice works out very well. The PCs SHOULD feel a bit intimidated and feel like they've messed with the wrong guy.
The rest of the mission is legwork part 2, where the PCs have ample opportunity to find the leads they need. Little can go wrong here, although they may skip a few scenes.
The last scene, the climax didn't go too well with me. Sure, the players didn't complain, but since I hadn't statted out all the insect spririts (I hadn't found them in Street Magic at that time), alot of the combat I basically just free-form'ed. Although I did it to save time, I regret it somewhat now as it just became too easy, especially because they PCs are armed and armored to the teeth at this point.
Oh, and I allowed them to wear heavy armor+helmet without reducing their stats for overburdening (otherwise only those with body 6+ would wear them), since Barrone wants to record the entire event with the secret simsense gear in the armors. Make sure the armor doesen't impeed the PCs and that they contain all available vision and hearing augmentations (including smartlink, unltrasound, vision enchancement - everything they want) so that they will use the armors. And allow them some equipment they normally wouldn't be able to get easily (such as a sniper rifle or assault cannon).
The initial fights are very easy since the 1st ed worker ant spirits are very weak, but if you use the 4th ed stats instead (but keep the force down) they will at least be some obstacle. They should at least feel they needed the armor, if not the extra guns.
Well that's all I can think of for now, keep asking questions and I can answer them if something's lacking or you wonder how I did something.
Cheers, FotD.