Wow, Sounds like a lot of fun! With your setup the only real hurdles I can see you running into would be getting your players to jump in the right direction when the drek hits the rotating blades and them being resentful when they find out that everything they knew was a lie.
It's been my experience that players, particularly Shadowrun players, will do things you never even considered. Make sure your hooks are big and bite deep. Also, don't be afraid to be blunt with your clues and hints, even intelligent people can be startlingly dim when playing and RPG.
As far as how they got into the experiment, I'd just tell them, when the time comes, that they had all volunteered for the program, and part of the experiment was giving them fake identities with falsified memories. I think people would accept that without too much balking.
Your adventure sounds like a lot of fun and very ambitious for a first time GM. My honest advice, if you haven't run any Shadowrun games before, is to run a few modules first and then go into your homebrew. It would be easy enough to just say that everything that had happened up to that point was also in the matrix.
Whatever you do, good luck and keep up the good work!
-Lodisy