The next day, cut it flush. Use a block plane to ensure it truly is flush. This will be the top of the bottom layer of the bench top, so gouges aren't a problem. (Wiping up glue with a damp cloth can lead to stains and finishes applying unevenly. That won't be a problem here, either.) But bulges and bumps are a problem - they will keep the two layers of the top from matching up evenly.
2 - use a plunge router with a bottom bearing cuter bit such as this from rockler: http://www.rockler.com/product.cfm?page=25160&site=ROCKLER .... I thought to use the short one as I plunge it directly downward in the centre of the hole until the bearing reaches within the tabletop hole. I suppose one could use a long one, but the stubbiness seemed more practical (the big bearing ensured accuracy?)
The hacksaw will often damage the last thread when it cuts. Running a nut off the end will fix this. You'll have to run the nut all the way down from the other end. This doesn't take long, if you chuck up the rod in your drill and let it do the work. Hold the rod vertically, with the drill pointing down, and just hold on to the nut enough to keep it from spinning.
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I decided to make my own top out of white ash because I had access to a planer and jointer at my local college where I was taking an intro woodworking class. Trim and vice jaws are white ash as well. Everything else is built pretty much as jdege describes. A plunge router with a 3/4" spiral up bit really made quick work of the dog holes. Finished with Danish oil.
2. Bill Hylton's Power-Tool Joinery by Bill Hylton. From the editors of Popular Woodworking magazine, this is a go-to for setting up power tools for making joinery. Organized by joint type - rabbets, half-laps, dovetails, etc - it provides detailed instructions show you how to make each joint with every tool possible. I especially like the jigs and fixtures details that show you there's definitely more than one way to skin that cat.
This table top is also made from the hardest wood out of any manufacturer we reviewed: oak. In fairness, this can be both a blessing and a curse. The oak wood is extremely durable and noted for its lack of a porous nature. This means the top can withstand plenty of abuse from tool and workpieces. Moreover, you will not have to worry about liquids like lacquers and stains from being absorbed into the top. That said, the hard oak can also do a number on tool sharpness, dulling them prematurely if they are not carefully handled.