Daughter has an ex-boyfriend who is secretly an Insect Shaman (Haven't decided what kind yet. Wasp?). The Ex-Boyfriend is obsessed with her, and wants to make her his Queen.
I would take a slower road for this (but the below is all just a suggestion). I would make the ex-boyfriend a "good merge" and the daughter is his first "recruitment" attempt which failed resulting in a kidnapping rather than recruiting. The whole reason he's an "ex" is because he joined a gang a few months back and the gang is a funnel for recruits for the actual hive. So the gang is a mix of mostly normals with a few good merges.
So when the players have to fight to get the girl back they fight a few members that are...odd. Odd both in capabilities and behavior. But mostly they're just fighting better-than-average geared gangers.
Unfortunately for the girl, the Insect Shaman for the hive had a chance (before the PCs ever get there) to look her over and thinks she's just perfect for the Queen's host so he's off at the main hive preparing things.
Next, throw a loop into everything by having the daughter not want to go back to daddy. She definitely doesn't want to go back to the gang, but she doesn't want daddy as well; either because he beats her, won't give her her inheritance from mommy's death, is too over protective, or something else (probably the reason why he doesn't want the authorities involved in the first place). So when the daughter offers to pay the runners to take her somewhere else...they have to decide to screw over their Johnson or help out the girl.
Their choice in how to help the girl will either lead to the Insect Shaman and her father trying to hunt them down (three-way combats can be quite fun) or the girl gets kidnapped from home again when the Shaman sends more "skilled" elements to get her back from her father (which would lead to the father hiring the runners again, seeing as how they did a good job the first time and didn't screw him over by helping the daughter). But in either case the insects work really really hard to make sure they re-kidnap the girl again.
Then once the girl is rescued a second time, some other Johnson has learned of the hive and wants the runners to destroy it (not to mention any other complications dealing with the daughter like "not you fraggers again, you're just going to take me back to daddy!").
This way you have levels in which to introduce the bugs. Level one, the gang, something is strange. Level two, the second kidnapping, it's dangerous at the hive. Then the third, destroying the hive, is deadly and scary. Once the players start to catch on that bugs may be involved you can have them notice the cockroaches in their kitchens, the wasps on their SuperJoySoda cans, etc.
As for your additional worry points:
a) The gang is well equipped, apparently by some corp, and once their contacts learn about the runners involvement with the gang, they'd be willing to pay big for information on who is supplying the gang.
b) Doing the first mission: assault the gang, get the girl leads to the next mission: get the girl from the insect shaman...which can lead to a third: great you got the girl but this other Johnson wants that hive destroyed.
c) Again, tiered missions...first one only one, maybe two, merged insect spirits (low to average force) and the mage isn't the star. Second mission, mage is needed for help against the shaman and his minions. Third mission the PCs may want to hire additional magical support if they decide to take the run to destroy the hive.
Again, just suggestions but something along these lines would help to address most of your worries. May you scare your players well
