Clamp the inner jaw of the end vise in position, leaving a little bit to trim off later, and then use the dowel and dowel center trick through the screw and guiide rod holes of the vise base plate to mark the position of the screw and guide rod holes in the jaw. Remove the jaw and drill 1-1/8" holes in the marked positions. I used the drill guide for most of the holes, and drilled freehand for the last bit. When you're starting a spade bit in a deep hole like this, start the drill very slowly, and the bit will move the drill into a perpendicular position. Start it too fast and the bit will bind and you'll damage the sides of the hole.
Before joining the top to the base, loosen the bolts and screws on the lower stretchers to create a little play in the leg posts. Align the top notches with the leg posts and tap the top into place with a hammer and piece of scrap wood, working evenly around the table until all leg posts are level with the tabletop. Tighten the lower stretchers and you’re done. A hefty thanks to Doug Merrill for this weighty idea.
So drill the benchdog holes through the MDF layer. Begin by laying out their positions. You'll want these to be precise, so that the distances between the holes are consistent. The vises you are using will constrain your benchdog spacing. My front vise worked most naturally with two rows of holes four inches apart, my end vise with two pairs of rows, with four inches between the rows and eight inches between the pairs. Because of this, I decided on a 4" by 4" pattern.
A shed is a great project to earn your sawdust legs on. It is just some very basic carpentry skills. You could build the whole thing with a circular saw, hammer, utility knife, pencil, and tape rule. Find a friend or relative that has some decent skills to help. You could do it in a weekend. Keep the size on a four foot increment to minimize wastee. I would recommend a 12 x 12 or a 12 x 16 if you can. If you don't want to cut any rafters (which is really a simple process), you can order small triangle shaped trusses for the roof from your local lumberyard. If you are using T1-11 for the sides, get the real plywood based stuff, no waferboard. Same thing for the floor, use plywood (treated if you like). Cedar for the trim, not pine. The visqueen underneath is a good idea. Insulate the walls inside to help temper temperature swings. Build overhanges into the roof all the way around, 12" is nice. These really are a fun project. You can add a small window with a flower box underneath to make it look a little homey too.
Out of all the shed books I have read, this book stays by my side while I hammer in the yard. The book is well written by what appears to be a non professional book writer (A Good Thing). It reads as if you are getting advise in laymans terms from your neighbor "The Craftsman", a welcome change from the DIY books, that assume a level of expertese. The level of detail is high and discusses gotcha's, advise, and trade "secrets" that could have only come from years of personal experience building sheds.