I wouldn't sweat it too much, cut out the old numbers and weld them into the new cowl, documenting everything as you go, before and after. I would not restamp the numbers, that is another can of worms entirely. Nothing wrong with repairing a rusty car, doesn't sound like you're moving numbers to a different chassis. Lots and lots of ebodies out there with cowl repair/replacement. Yes there are diffences in the cowls year over year, and also not sure if the repops are 100% accurate or not. Compare the old and new side by side and note any differences, correct them if possible to be authentic. No VIN#s are stamped in the trunk rails on ebodies.