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.

I don't see anywhere you mentioned the over all length of the bench top. A piece of 1 1/2" x 25" x 8' glued edge oak at Lumber Liquidators costs $192 including tax. Two piece is almost $400! Would that be better if I use two IKEA 1 1/4" x 25" x 74" solid Beech ($99 each plus tax) on top of a layer of 3/4" Birch plywood. That would be 3 1/4" over all.
Palomar Community College in San Marcos, located about 35 miles north of San Diego, offers certificate, degree and life-long learning programs to more than 20,000 students a year. In particular, the Cabinetmaking and Furniture Technology Department offers in excess of 50 classes annually, and the present faculty is composed of four full-time teachers, 21 part-time instructors and 11 teaching assistants. As of Fall 2013, woodworking students will have access to a newly remodeled woodworking facility equipped with three machine rooms, three bench rooms, a saw mill and a finish room.
Workbenches have flat tops, though sometimes at the rear there is a cavity called a tool well that contains tools and components (and prevents them from falling off). One advantage of having the well set into the top of the bench is that, even with a variety of objects in the well, a large sheet of material can still be laid flat over the entire surface of the bench; the contents of the tool well offer no interference.
After you have all the holes clean, set things up for your glue-up. You want everything on-hand before you start - drill, driver bit, glue, roller or whatever you're going to spread the glue with, and four clamps for the corners. You'll need a flat surface to do the glue-up on - I used my hollow core door on top my bench base - and another somewhat-flat surface to put the other panel on. My folding table was still holding my oak countertop, which makes a great flat surface, but I want to make sure I didn't drip glue on it so I covered it with some painters plastic that was left over from the last bedroom we painted.
The book is well written and easy to read. The illustrations, I'm sure were excellent in 1914 and, are still adequite now. Most of the designs seemed repetitive, though. I wish more attention had been given to lashing materials. If you are looking for that you will find almost none here. The book was fun to read and provided enough inspiration to make my brother and me attempt a large hut.
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