Why is a Aztech Johnson fronting for a Lone Star detective? Supposedly to build up favors for future moves. So he helps a low level detective who is distrusted/hated by his own supervisors and the media? Yeah, great guy to have owe you favors.
When you're trying to build a presence, you don't start with the people already at the top. They've already got their positions and power, and aren't going to be as beholden to you for small favors. Now, you take someone who is somewhat on the outs, but still has some standing (he's still a Lone Star detective, after all), and give him a couple big breaks? Suddenly, you got someone who may be poised for a rapid rise, and they'll know exactly who they have to thank for it. And since corps are moving back to Chicago, having sources in the local law enforcement will be key for making things go smooth.
The lab research involves cloning and networking technomancers. So why did they put a "kill everyone" suite of delta grade bioware into the original, nearly destroying her Resonance abilities?
The lab research involved very early research into mind-machine interfaces, even before the Otaku came to be. Remember, back in 2052, no one knew anything about the Otaku, and certainly not about Resonance or Technomancers. Hell, Renraku was still trying to crack how to make a functioning AI way back then. So they probably didn't know they were destroying the original's abilities. As for the bioware/geneware, think about it for a second. You've found someone with an inherent, unhackable connection to the Matrix, and you got her as a child. If you can turn her into a living weapon and control her, then you've got a powerful weapon in the corp wars (which were still going on back then) that won't show up on any cyberware scanners or metal detectors.
Since when are cranial bombs removable by people without medical training, operating with an arm twisted behind their head, viewed through a camera, and with no pain medication, without triggering the anti-tamper circuits? (I can't believe they didn't give her a pain editor, BTW, given all the other Mary Sue crap she has.)
You don't think the free sprite she had helping her maybe hacked the bomb to make sure it didn't go boom while she was taking it out? As for taking it out itself, a kink bomb at the base of the neck wouldn't require too much knowledge to remove, unlike one planted under the skull. But that's not what we're talking about here. At the base of the neck, with sufficient adrenaline and looking at it through a camera, you could do it. Wouldn't be easy, but you could do it. The Medicine skill is used to properly remove cybernetics without causing further damage. Nothing is stopping you from taking a knife and digging the things out, or ripping the cyberarm off a guy and beating him with it, for instance.
How did a facility in the CZ, whose parent corporation doesn't apparently remember they exist, fund and acquire delta grade bioware so easily that they can waste it on incomprehensible uses?
Shiawase didn't always not know about the lab. And remember, it never said when in those twenty years the girl got the modifications done. If I had to guess, I'd say it happened sometime between Ares spraying the area with FAB III, and Crash 2.0. Wartorn wastelands are great places for hiding experiments like this.
Why doesn't Shiawaise know about this facility, giving SK the opportunity to steal it? Why isn't there any discussion of the runners thinking of calling Shiawaise in search of a much better pay day, or at least renegotiating with SK?
There's been plenty of turmoil in Shiawase over the years. The board has changed several times, one of their family is the Empress of Japan, there's been internal squabbling in several of their divisions, including their intelligence division, the different factions of the Shiawase family are still fighting eachother, and more. Then you have this little thing called Crash 2.0, where god knows how much data (like property registries) was lost or corrupted. And even before that, we're dealing with the CZ, where things were a mess to begin with. Assuming this was a 'black', off-the-books project, that's easily enough to cause it to be forgotten.