Put the countertop on the base, put the MDF on top of the countertop, and line up the marks you drew on each end of the MDF with the countertop below it. When you have it lined up, clamp things down, and route the edge of the MDF using a 1-1/2" or longer flush-trim bit, with the depth adjusted so the bearing rides on the countertop. I clamped a couple of scraps of doubled MDF at each end to give the router base something extra to ride on at the ends.
The top is supported by the top ends of the legs and the top sides of the top stretchers. Stand your legs on end on a flat surface (like my door) and see if they wobble. If you have an end that isn't quite stable, use it as a foot, where the leveler will make it's flaws unimportant. Check the top edge of each stretcher for straightness. If one has a bit of a bow, use it for a lower stretcher. It's less critical that the shelf be well supported along its length.
Traditionally woodworkers (joiners) learnt their craft working as an apprentice in the Master Craftsman's shop doing the grunt work and learning by assimilation over many years. Our approach is a little different. We're making the assumption that you're smart; are developing or already have a passion for woodworking; and can devote three months to intensive learning.
I agree that I might quickly outgrow a 12x8 shed. Lowes also offers a 12x10 Rancher (same style, but more room), but the 12x10 is 9 feet, 4 inches high, and my community only allows a maximum height of 9 feet. The 12x8 is exactly 9 feet high. I'm afraid of getting "out of spec" if I exceed the height limit and then getting in trouble with the Home Owner's Association. Having said that, 12x10 would be about the biggest size I could get for the available area in my back yard, so even if I hire a shed contractor to do this, the shed would have to be 12x10 or smaller.
Next is the shelf. Start with the 24x48" piece of MDF. Clamp this on top of the base, and pencil in the outside of the stretchers and the inside angle of the legs. Flip it over, pull out your trusty cutting guide, and cut it to width and to length. Cutting out the angles is simple, with a jig saw. It's not much work with a hand saw. If you took enough care with supporting blocks and stops, you could probably do it with a circular saw. Since I did have a jig saw, I used it.
Then I flipped the top and the base, lied up the base in the proper location relative to the top, I then positioned the front vise and the support MDF for the end vise, and marked the locations of the bolt holes. Then I flipped the base right side up, drilled small pilot holes from the bottom side where I had marked the locations, and then drilled shallow countersink holes from each side, then a through hole that matched the bolts. Finally I tried out the bolts and washers, and deepened the countersinks until the heads of the bolts were just below flush.
A woodworking school teaching furniture making techniques located in Pennsylvania. Beginner through advanced students will learn solid wood furniture construction using traditional and modern techniques. The classes emphasize wood movement, practical methods, efficiency (with machines and hand tools), design, milling, joinery, finishing, and safety. Woodworking and furniture making courses are offered to aspiring crafts men and women throughout the country.