With the shelf secure, get a couple of friends to come help, and stand the bench on its feet. I said earlier moving the top by yourself is dangerous. Trying to lift the entire bench is foolhardy. Of course, I already said I'm stubborn, so I did it myself by rigging a simple block-and-tackle using lightweight pulleys I got at the hardware store. (Not the lightest-weight pulleys, those are meant for flag poles and have a design load of something like 40 pounds. These had a design load of 420 pounds.)
If you're using drywall screws, you'll want to countersink the holes. Drywall screws are flat-head, and need a countersink to seat solidly. If you're using Kreg pocket screws, the way I did, you won't want to counter-sink the holes. Kreg screws are pan-head, and seat just fine against a flat surface. Both drywall screws and Kreg pocket screws are self-threading, so you don't need pilot holes in the second sheet of MDF.
I would say take the shed, you'll find some use for it. I have contemplated this question also. I have a 20' x 11' basement shop, thats quickly loosing space. If you live in an area with a harsh winters (say the midwest), does it make sense to heat the shop through the week if you are only working in the shop on the weekends? Or do you run the heaters just when you are working in the shop? What kind of heaters are recommended (radient, wood stove, etc.)?
I marked out the one hole location, drilled a shallow 1/16" hole into the top. I then put a 1/16" bit through the hole in my template and into the hole I had just drilled. I lined up the template, and drilled a second hole, then put another bit through that. From then on, I worked entirely from the template. With two bits through the holes pinning the template in place, the other holes in the template would be precisely located (or so the theory goes) on a 4x4" grid.
Something like this really does look like it would be a fun project. I guess I need to go out to the yard and use some stakes and brightly colored taped to mark off some different dimensions (12x8, 12x10, 12x12, etc.) to figure out just how big I can make this thing. If I'm building it myself, it'll be easy to keep the height right at the 9 foot limit.