Cut the steel cowling hinge pin in half to use for hinge alignment.
Reinstalled the upper cowl with the hinges clecoed on and the pins in place. Dorking with the upper left engine mount bolt had zero effect on the alignment. Put the lower cowl back in place, clamping it tight with a tie down strap. Noted an area on the left upper seam that needs a bit more sanding, and the location for a notch to allow hinge pin clearance.
Took the lower cowl off, sanded a bit, reinstalled. Getting very close. Did another iteration to smooth the mating surfaces where the hinges will be installed, and fine tuned the hinge pin slots.
Reinstalled. Getting very close.
I think it might be ready to drill the lower cowl for the hinges -after a couple iterations, of course. After that, it will be time to start installing the MilSpec fasteners.