The Boston Lockdown book has a lot of extra info about CFD, and Market Panic takes a gorgeous look at where the megas are today and what their agendas are.
If you still aren't married to a specific mega yet, here are a few considerations.
NeoNet CFD is pretty much their fault. It was a joint project along with Evo and Aztechnology, but the whole thing was Celedyr's baby. Evo actually seems to be taking more heat from it because they've been taking in CFD infecties who have been ejected from their parent corps (and making bank because of it) which makes it seem like this was their plan the whole time, but NeoNet is not above suspicion, and in 2077, they're really starting to fall apart as important people are jumping ship. They're third A is in real danger, so a team of corporate dudes would have a lot of jobs to help the company hang onto their status. They would also have a lot of jobs dedicated to finding, destroying, and scrubbing evidence of NeoNet's connection to CFD. On top of that, the way they're splintering means you could have a team who works directly for one of the big players, and give them jobs aimed towards salvaging as many pieces of NeoNet as they can for their employer to take with them when they change horses. Of particular note is that they seem vulnerable enough that other corps are soliciting Richard Villiers, hoping to get the seat on the CC that comes along with JRJ ownership in their stable. Lot's of fun to be had there.
Evo As mentioned, Evo is coming under a lot of fire, and they're the other mega most at risk of being downgraded to a AA right now. They were definitely involved in CFD, but not as much as NeoNet, so they're going to want to get their hands on anything they can to shift blame onto their recent partner and off of them, and what they have going for them is that the evidence is there, it's just very closely guarded. The fact that they have taken in rogue head cases from the R&D divisions of their rivals has allowed them access to a lot of sensitive information as well as given them a windfall of bleeding edge technical expertise that's now giving them the resources to put out new tech that we would have been decades away from otherwise. Could be some fun and potentially dangerous toys there for your players.
SK: They have nothing to do with CFD, but Lofwyr is furious about it and he wants to see heads role. You could conceivably have the party playing an SK Prime unit whose main goal is to find out who is responsible for the virus, and why.
Ares: The thing about their gung-ho streak is that it's what you see in their militaries. If you want them doing black ops, that's something they can't afford. Being gung-ho gets you noticed, and when your guys get noticed, you need plausible deniability. That's what shadowrunners are for. However, that does bring us to...
Renraku: They have a thing for stability, including in their runners. Something that they've played up in sourcebooks recently is how after several successful runs, Renraku Johnsons prefer to place their best runner teams on retainer, eventually grooming them to become company men, and you could have a party who begins in this situation. For extra fun, the Red Samurai HATE these guys. Like they say in Run Faster, the Red Samurai are the jealous wife, and the runners are the mistress.
Shiawase: I mention them because you said you wanted to do stuff with CFD and you also had a soft spot for the Japanacorps. There has been mention that because Shiawase has long been a pioneer in nanotechnology, people have been expecting a cure or vaccine from them.
