We decided to add 2 inches to the bottom part of the large soils shear box and 2 or 3 inches to the top box. We ordered the steel and I had to drill and tap holes to attach the extension. I also drilled and tapped holes holes for the loading cylinder. I layed out a hole pattern on the top of the extension. We decided on 3 bolts in one direction and 4 in the other equally spaced out. Then I drilled out the hole to the tap drill size 5/16th for 3/8th inch bolt, and then recessed it to where a bolt can fit in there. I then clamped this piece to the other box. I was going to use a center punch and mag drill, but the mag drill was proving too unwieldy in this situation.
I drilled a hole dead center on a 5/16th inch bolt and dropped it hole, this creates a centered pilot at equal depths. After that I would take a 5/16th inch drill bit and chase it. If you do everything in order you will get evenly drilled holes and very similar depths. I then tapped all of the holes with a 3/8 inch tap.
Finished product, all bolted together.