David, Yes, get the bolts long enough to go through every thing without any threads chewing things up. Are you going to weld outside support bushings on the plates? If you are using any long bushings, make sure that you have grease fitting installed.
I checked out some hole cutters, and found out some things.The quality ranges from good, better, best, and very best. The basic hole saw had straight teeth, and the one that you bought have offset teeth. They also make some with carbide teeth. I bought one of these, and will be checking out how well it works. It cost $18.00 . The annular carbide cutters, will cut better, but cost about $95.00 . They are used for drilling through things like I-Beams, using those magnetic hole-hawg drills. Some people say the trick is to keep the bit cool with water, kerosine or cutting fluid.
I will probably use a mixture of bolts and pins.