Buy a wheel with the right size axle hole, and use that. I did that for the 1/2" holes to mount my nice new vice, and it worked great. The rubber sides of the tire are a perfect grippy base to keep it from wandering. You only need one size, right?
Use a drill that has a built-in bullseye level. That’ll get you very close to vertical. And drill the hole a scosche bigger than the bolt so that there will be room for the bolt to right itself when you screw the nut on.
What wood did you use for the bench top? The base?
Where did you get the plans for this beauty? Nicely crafted.
The base is beech. The top was purchased pre-made by a local supplier, although I had to route the ends square. The project was done in a week-long woodworking class setting. Because of the space and time constraints, we just couldn’t make the tops ourselves. All the rest - the stretchers and trestles - was made by class participants. Again, because of time restraints, the lumber was milled by shop staff. The stretchers gave me fits, by the way. I spent an entire afternoon trying to get the mortises and tenons to fit properly. Most of the joinery done in these classes is done by hand. Larger cuts, like the tenons on the stretchers were rough-cut on a large band saw, but finished by old fashioned grunt work with planes and chisels. Did I mention that beech is freaking hard? 
ETA: the wedges are also beech, stained walnut for accent.
Fir na tine: Plan copies were provided by the studio. The owner of the place, Gary Rogowski, most likely designed the bench himself. He’s a pretty well-known master woodworker, having written a couple of books on the subject. You might try contacting Northwest Woodworking about obtaining a copy. I really have no idea if they charge for such things.
I have his Complete Illustrated Guide to Joinery, great book, demystifies the subject of joining wood very well. I wish there were woodworkers like him teaching in my neck of the woods.
He knows his stuff, alright. As a teacher, he’s a bit impatient, which, for a paying customer, can be annoying. Since we are there to learn, having the teacher be dismissive is a significant downer. I think he realizes this shortcoming and will usually try to make amends in some way. It may be that there is a grudging realization that they have to offer these classes as a way to help keep the doors open, even though they have a Master program and do commissioned pieces. Surprisingly, it’s one of only two woodworking schools in Portland (not counting a very expensive community college program). I’m glad it’s there and I can deal with a bit of grouchiness in exchange for the opportunity to learn something new.
Too bad he’s not in the original Portland area. Maine, that is!
Nice bench indeed. Shame to drill holes in it.
I’ll second FordPrefect’s suggestion of using an auger. Beats my Forstner bit idea.
My wife wanted to bring it in the house for a dining room table. 
Drills often have a spirit level to help keep the alignment straight. My Dewalt has that feature and it helps.
Check this out. In the second photo he shows a beam borer. In the third photo he modified a portable drill/stand.
In this thread, a dowel jig was used.
That beam borer is pretty cool. You also get a workout after 12 holes.
you could clamp up roasts in the vise for carving.
Don’t worry, she will change her mind after you’ve drilled 20 holes through the top, chipped the edge, made more than a few chisel gouges into the top, and generally turned your bench from fine furniture to a fine workbench.
I hope your bench works out for you, the style you chose is not in line with the current fad of building a Roubo. My current bench is 2.75" thick douglas fir, while I am not totally convinced on the Roubo style, my next bench is going to have a 5" thick hard maple top, it’ll be 10 - 12’ long and be able to leap tall buildings in a single bound
The beech used for the base will beef that sucker up though, but, worst case if you have too much racking when planing, you could add a Shaker-style cabinet to make it more solid.
These are the same benches used in Rogowski’s shop and they’re rock solid. Between the wedged tenons and the buttons, nothing much moves. There will also be a plywood shelf on the stretchers, which will help stop any movement.
A strong argument for using beech in my future super bench!
What’s the first project planned for your new shiny bench?
No idea. I have very limited space for shop tools and I mainly wanted a good bench for doing any sort of work, not just limited to woodworking. Just trying to use my chop saw involves a lot of gymnastics and cursing, but now I can just set it on the bench. I’ve been kicking around the idea of doing a guitar project, but don’t have any specific things in mind. The problem with making things is then finding somewhere to put them. Tiny house, no room. It’s the one curse of downsizing.
…or as the old sailors say, “Avast!”