ok so basically, your gonna seperate a compartment thats maybe 1/3 or 1/2 of what the bottom area is now... so you'll still be left with storage space...
once you have it sectioned off, i would suggest throwing up some panda plastic (the black and white poly) to make it completely light tight against the upper area... don't want any light leaking into the flowering girls above ya know!
and basically, for lighting i would use a couple 4ft shoplights (each holding 2 four ft t12 floro tubes) if you have the room to fit them in there, and if not, then you can use some cool spectrum cfls also....
now, your still gonna need to vent the clone room... but a couple strong computer fans hooked up to some short tubing for both the intake and outake will take care of that...
then you just need a little propagator in there... and i'll leave the cloning methods to you... but that'll give you a nice place to do it in...