Should I make the hive 36" or 48"?
I think you will want the extra space in the 48' size. The smaller the hive, the more carefully you will have to manage it. In the 48" length you can fit in about 33 frames, roughly the equivalent of 3 Langstroth boxes. Unless you would normally prefer to be limited to fewer frames than that, I would not go smaller.
Also, if you put entrances at both ends of the box, you can have two smaller colonies in the box at the same time. We have found that versatility to be very useful.