Hey there,
Seems like you have a pretty solid idea on how you plan on setting up the PCs. First, the general premise of the Run seems to be rather run-of-the-mill and so it's feasible that your players won't see the double-cross coming. Simple extraction, big nuyen, few problems foreseen. A good premise.
The first thing I would, were I you, start thinking about is pertaining to what sort of assets this Blood Mage has: how far does his influence reach, how many other "puppets" (like the Johnson you mention) does he have set up. Writing a list and working through the logistics of that character's influence might very well give you more material for you to work with -- The more material you can think up, the more likely the Blood Mage will be able to spread his influence around matters concerning the Shadowrunners' group.
Now, about your Johnson...
Intel the Johnson might reasonably have on the company they're running against (I'm going with a single/double A, not a major player)
It is very likely the Johnson has a network of contacts with whom he operates either within the company whose interests he represents or without. A good place to start in relation as to how far-reaching his personal "web" of influence spreads would be to list those contacts and elaborate on their relationship with the Johnson. Doing this, you can then likely begin penning down what sort of information the Johnson has access to.
Remembering that many Corporations also own and work behind several subsidiaries, you could make the target of the Run a company of your choosing's front. That way, the Johnson's intel might relate to that front without necessarily give any information on the Corporation behind it -- maybe he simply doesn't know it's a subsidiary of a bigger company behind the scenes, or maybe he has an idea of it but doesn't have access to the particulars, etc.
Info could be, for example, the type of products and services the company provides, the whereabouts of the company compound they will have to infiltrate, a general idea of the sort of security measures the Runners might feasibly encounter. Injecting a bit of misinformation at this point would work well to set up the intended double-cross. Say, the Johnson says that the company sometimes hires Knight Errant security as backup when, in truth (the Runners can learn this by doing some legwork), it's more to do with the Lone Star.
Ways to tip them off that things mightn't be all that they hoped without spelling it out or spooking them (preferably when they're too late to pull out)
Working the angle I suggest above might be a way to tip them off, should the Runners' legwork find some discrepancies with what information the Johnson revealed. The key here is to try and be subtle, as anything too glaring should immediately rouse suspicion. You want to avoid that. Just think of minor things that may not be entirely true that the Runners can cross-check upon and verify.
Word on the Street might also speak about something to do with the Johnson's-Real-Name (info the Runners probably don't have as Johnsons typically don't give their names) being involved in some ugly business (his association with the Blood Mage) beyond the bounds of the company he represents. Again, this Street Rumor-mill might not be entirely accurate, but may give insight without actually spoiling anything.
If you prefer the Runners learn these things while effectively "inside" the Run, you could leave some files or data around that has been hastily hidden. Emails between the Johnson and the Blood Mage (or any similar electronic evidence of communication). Using nicknames to hide their identities behind would be helpful in allowing the Runners to piece some things together without actually getting the entirety of the information. The best way to work on revealing a plot or intrigue to the players is, in my experience, making it piecemeal and like a puzzle they need to solve.
And other tidbits about the noble art of setting up your players and then betraying them while they glare at you which you consider of worth.
Keep them informed on what's going on through their legwork and data finds, but inject some misinformation or oblique interpretations in whatever data they get their hands on that may relate to what's going on behind the scenes. Another good way is for them to become friendly with a contact who's a contact of a contact working for Whoever-Will-Set-Them-Up. The logic behind using double-agents is that whoever has interests in double-crossing someone usually will want to stay informed about their dealings and whatever they may be up to.
Just some ideas for you to consider (if you hadn't already).
