Luke, the differences are not formidable, but if she wants bone stock, then of course you'd want original equipment fir judging purposes. Going with the '46 assembly will move the wheels outward by 7/8" each side. The axle ratio may actually be more preferable in the '46 than as the pickup may have, as pickups were generally geared lower than passenger cars. Spring hangers are the same for both, but again, pickups would have stiffer springs than passenger cars. '41 shocks are Houdaille as are the '46 shocks, but with minor differences also. Even if you built it with all the '46 components, it would take an expert to tell the difference.
Taking this a step further, you probably have an open driveshaft in the conversion, which would have to be changed out to torque tube as original. This will require a transmission to match, which are readily available, but you see how the list can get long depending on how the truck is set up as it sits today.