I don't know what model GT40 you have. If you shorten the tops of the pins you may not have anything for the Allen wrench to work with.
The pins are under Shear and tensile loads. I wouldn't cut or grind anything that gives you less thread engagement at the hubs or studs.
The ERA 427 Jag hub is shown
http://www.erareplicas.com/427man/wh...drive_hubs.pdf
If your GT40 does use Jag hubs these shorten 6 pin hubs from Vintage Wheel would tuck your wheel 1.0" per side.
https://vintagewheelsus.com/index.ph...roducts_id=521