OMG! and you say you have only a limited time to work on it?
*whew* that is a lot of rooms. If it were me, I would have made something about half the size of a single level (spread out over the nemerous verticle levels) and called it a day.
What you made is extremely ambitious. Kudos to you if you can fill it.
Anyway, to answer your question...
What about making a random table, each level could be a different list of encounters. Also, have a few short lists of stuff to find, and have a few lists of stuff to find stuff in ;-) Then have sub lists for variation.
Stuff in rooms
Locker
cabinet
closet
safe
Stuff in stuff in rooms
medical
weapon
armor
device
sublists
medical
medkit
neural spray
skinfoam
regerant
harmful chemical
device
communicator
tracker
helpbot
laptop
etc.