Looking great so far, Debbie. . You have accomplished the hardest part of making boxes with box jointed corners, and that is getting the pin widths and pin spaces to fit together well..
Is your box glued together yet? Have you thought about how to attach the top and bottom? Solid wood tops and bottoms change size with humidity changes, and if just attached to the box sides with glue they will either split or break free with humidity changes. It's best to cut a dado into the box sides and fit the solid top and bottom into these dados without glue as the box is assembled and corner glued. This lets the solid wood panel change in size as the humidity changes without breaking the box.
Plywood is more dimensionally stable than solid wood, so in most cases you can just glue the plywood tops and bottoms to the box sides without a problem, but the disadvantage to this is that the box appearance will suffer, because the plywood edges will show, unless installed in dados like the solid wood panels.
Now to answer your question about trimming the pins to length after gluing -
I place a scrap piece of 3/4" thick wood on my router table top attaching it in place with double sided tape. This is a spacer to hold your box above the router table. I locate it about 2" from the router bit. A flush trim router bit with an end bearing is installed. I then place one of the assembled box sides on this board so that the pins of one side of the corner hang down between the board and the bit, and set the height of the router bit so that the bearing rides on the smooth box side above the pins to be cut. Use a piece of scrap as a pusher and feed the pins into the spinning bit. The pusher block should protect the last pin from chipping as you cut this last pin and cut into the pusher block. Then flip the box and repeat to flush trim the excess pins from each side of each box corner. A light to moderate sanding should make the pins perfectly flat and smooth. I usually use my Random Orbit Sander and 150 grit paper for this.
If you go with just gluing a plywood top and bottom to your box sides, make each about 1/4" larger all the way around.It's easier to position and glue correctly this way. Then flush trim this excess off on the router table with the same flush trim router bit. Sand the edges smooth with the ROS and 150 grit paper.
Central North Carolina