Considering the way the rearends sit about 1.5" forward in the rear wheelwells of a '41 I'd go slightly longer, not shorter. A wheelbase that centers the axle in the rear will give a nicer looking rod when finished.
I'd not start from scratch with a frame unless you really feel comfortable doing so. The rear is not as hard, but getting the geometry correct and square is important, and using a donor front frame will ensure it's not only right, but it will use all factory parts when you need anything later.
I'd go with any GM front frame or subframe that is the right width, and mate it to your stock frame. In the rear I'd use the stock frame, but build new spring perches to locate the axle center, and use an axle and springs from a donor car to fit to your modified frame mounts.