I was not satisfied with the fit of the longerons at the aft end and was concerned that the small amount of material extending past the last bulkhead may interfere with mounting the vertical stab. I put the longerons back in the aft fuselage and marked for trimming. Removed left longeron and I used the small dremel sanding drum to trim the longeron and blend in to the radius. Used a file to straighten the edge. Reinstalled the left longeron and the fit was flush. Repeated process for the right longeron.
Per Wirejock's advice I reamed all the holes in the longerons before I started countersinking. Had to move things around the shop to find ways to support the longerons for this work. Also used one half of the Bueller die to help clamp the longeron to the bench. With all holes reamed, the countersink ran very well in the holes and I countersunk all holes in both longerons with no issues. Scuffed the longerons with scotchbrite and washed them to prepare for priming.