I think it's going to be pretty tough to pull that off, especially given that the original panels weren't made to tight tolerances. Mis-alignment of striping will be very noticeable even if off by only 1/32" of an inch, but I guess that depends upon your eye for detail.
Is there any way you could mount, shim, and align the panels and doors for the final fit, mark the location for the masking, and then take them off to paint? You'd have to be careful to use the same shims for the fenders in the same locations when you go to re-assemble.
1980 Pontiac Sunbird, 2.5L Notchback Coupe